Annotation of imach096d/src/imach.c, revision 1.86
1.86 ! brouard 1: /* $Id: imach.c,v 1.85 2003/06/17 13:12:43 brouard Exp $
1.83 lievre 2: $State: Exp $
3: $Log: imach.c,v $
1.86 ! brouard 4: Revision 1.85 2003/06/17 13:12:43 brouard
! 5: * imach.c (Repository): Check when date of death was earlier that
! 6: current date of interview. It may happen when the death was just
! 7: prior to the death. In this case, dh was negative and likelihood
! 8: was wrong (infinity). We still send an "Error" but patch by
! 9: assuming that the date of death was just one stepm after the
! 10: interview.
! 11: (Repository): Because some people have very long ID (first column)
! 12: we changed int to long in num[] and we added a new lvector for
! 13: memory allocation. But we also truncated to 8 characters (left
! 14: truncation)
! 15: (Repository): No more line truncation errors.
! 16:
1.85 brouard 17: Revision 1.84 2003/06/13 21:44:43 brouard
18: * imach.c (Repository): Replace "freqsummary" at a correct
19: place. It differs from routine "prevalence" which may be called
20: many times. Probs is memory consuming and must be used with
21: parcimony.
1.86 ! brouard 22: Version 0.95a3 (should output exactly the same maximization than 0.8a2)
1.85 brouard 23:
1.84 brouard 24: Revision 1.83 2003/06/10 13:39:11 lievre
25: *** empty log message ***
26:
1.83 lievre 27: Revision 1.82 2003/06/05 15:57:20 brouard
28: Add log in imach.c and fullversion number is now printed.
29:
1.82 brouard 30: */
31: /*
1.53 brouard 32: Interpolated Markov Chain
33:
34: Short summary of the programme:
35:
36: This program computes Healthy Life Expectancies from
37: cross-longitudinal data. Cross-longitudinal data consist in: -1- a
38: first survey ("cross") where individuals from different ages are
39: interviewed on their health status or degree of disability (in the
40: case of a health survey which is our main interest) -2- at least a
41: second wave of interviews ("longitudinal") which measure each change
42: (if any) in individual health status. Health expectancies are
43: computed from the time spent in each health state according to a
44: model. More health states you consider, more time is necessary to reach the
45: Maximum Likelihood of the parameters involved in the model. The
46: simplest model is the multinomial logistic model where pij is the
47: probability to be observed in state j at the second wave
48: conditional to be observed in state i at the first wave. Therefore
49: the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
50: 'age' is age and 'sex' is a covariate. If you want to have a more
51: complex model than "constant and age", you should modify the program
52: where the markup *Covariates have to be included here again* invites
53: you to do it. More covariates you add, slower the
54: convergence.
55:
56: The advantage of this computer programme, compared to a simple
57: multinomial logistic model, is clear when the delay between waves is not
58: identical for each individual. Also, if a individual missed an
59: intermediate interview, the information is lost, but taken into
60: account using an interpolation or extrapolation.
61:
62: hPijx is the probability to be observed in state i at age x+h
63: conditional to the observed state i at age x. The delay 'h' can be
64: split into an exact number (nh*stepm) of unobserved intermediate
1.66 brouard 65: states. This elementary transition (by month, quarter,
66: semester or year) is modelled as a multinomial logistic. The hPx
1.53 brouard 67: matrix is simply the matrix product of nh*stepm elementary matrices
68: and the contribution of each individual to the likelihood is simply
69: hPijx.
70:
71: Also this programme outputs the covariance matrix of the parameters but also
1.54 brouard 72: of the life expectancies. It also computes the stable prevalence.
1.53 brouard 73:
74: Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
75: Institut national d'études démographiques, Paris.
76: This software have been partly granted by Euro-REVES, a concerted action
77: from the European Union.
78: It is copyrighted identically to a GNU software product, ie programme and
79: software can be distributed freely for non commercial use. Latest version
80: can be accessed at http://euroreves.ined.fr/imach .
1.74 brouard 81:
82: Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
83: or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
84:
1.53 brouard 85: **********************************************************************/
1.74 brouard 86: /*
87: main
88: read parameterfile
89: read datafile
90: concatwav
1.84 brouard 91: freqsummary
1.74 brouard 92: if (mle >= 1)
93: mlikeli
94: print results files
95: if mle==1
96: computes hessian
97: read end of parameter file: agemin, agemax, bage, fage, estepm
98: begin-prev-date,...
99: open gnuplot file
100: open html file
101: stable prevalence
102: for age prevalim()
103: h Pij x
104: variance of p varprob
105: forecasting if prevfcast==1 prevforecast call prevalence()
106: health expectancies
107: Variance-covariance of DFLE
108: prevalence()
109: movingaverage()
110: varevsij()
111: if popbased==1 varevsij(,popbased)
112: total life expectancies
113: Variance of stable prevalence
114: end
115: */
116:
117:
118:
1.53 brouard 119:
120: #include <math.h>
121: #include <stdio.h>
122: #include <stdlib.h>
123: #include <unistd.h>
124:
1.86 ! brouard 125: #include <sys/time.h>
! 126: #include <time.h>
! 127: #include "timeval.h"
! 128:
1.53 brouard 129: #define MAXLINE 256
130: #define GNUPLOTPROGRAM "gnuplot"
131: /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
1.85 brouard 132: #define FILENAMELENGTH 132
1.53 brouard 133: /*#define DEBUG*/
1.85 brouard 134: /*#define windows*/
1.53 brouard 135: #define GLOCK_ERROR_NOPATH -1 /* empty path */
136: #define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */
137:
138: #define MAXPARM 30 /* Maximum number of parameters for the optimization */
139: #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
140:
141: #define NINTERVMAX 8
142: #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
143: #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
144: #define NCOVMAX 8 /* Maximum number of covariates */
145: #define MAXN 20000
146: #define YEARM 12. /* Number of months per year */
147: #define AGESUP 130
148: #define AGEBASE 40
1.85 brouard 149: #ifdef unix
150: #define DIRSEPARATOR '/'
151: #define ODIRSEPARATOR '\\'
152: #else
1.53 brouard 153: #define DIRSEPARATOR '\\'
154: #define ODIRSEPARATOR '/'
155: #endif
156:
1.86 ! brouard 157: /* $Id: imach.c,v 1.85 2003/06/17 13:12:43 brouard Exp $ */
1.81 brouard 158: /* $State: Exp $ */
1.80 brouard 159:
1.84 brouard 160: char version[]="Imach version 0.95a2, June 2003, INED-EUROREVES ";
1.86 ! brouard 161: char fullversion[]="$Revision: 1.85 $ $Date: 2003/06/17 13:12:43 $";
1.53 brouard 162: int erreur; /* Error number */
163: int nvar;
164: int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
165: int npar=NPARMAX;
166: int nlstate=2; /* Number of live states */
167: int ndeath=1; /* Number of dead states */
168: int ncovmodel, ncovcol; /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
169: int popbased=0;
170:
171: int *wav; /* Number of waves for this individuual 0 is possible */
172: int maxwav; /* Maxim number of waves */
173: int jmin, jmax; /* min, max spacing between 2 waves */
174: int mle, weightopt;
175: int **mw; /* mw[mi][i] is number of the mi wave for this individual */
176: int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
1.59 brouard 177: int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
178: * wave mi and wave mi+1 is not an exact multiple of stepm. */
1.53 brouard 179: double jmean; /* Mean space between 2 waves */
180: double **oldm, **newm, **savm; /* Working pointers to matrices */
181: double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
182: FILE *fic,*ficpar, *ficparo,*ficres, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
1.76 brouard 183: FILE *ficlog, *ficrespow;
1.85 brouard 184: int globpr; /* Global variable for printing or not */
185: double fretone; /* Only one call to likelihood */
186: long ipmx; /* Number of contributions */
187: double sw; /* Sum of weights */
188: char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
189: FILE *ficresilk;
1.53 brouard 190: FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
191: FILE *ficresprobmorprev;
192: FILE *fichtm; /* Html File */
193: FILE *ficreseij;
194: char filerese[FILENAMELENGTH];
195: FILE *ficresvij;
196: char fileresv[FILENAMELENGTH];
197: FILE *ficresvpl;
198: char fileresvpl[FILENAMELENGTH];
199: char title[MAXLINE];
200: char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH];
201: char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
202:
203: char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
204: char filelog[FILENAMELENGTH]; /* Log file */
205: char filerest[FILENAMELENGTH];
206: char fileregp[FILENAMELENGTH];
207: char popfile[FILENAMELENGTH];
208:
209: char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];
210:
211: #define NR_END 1
212: #define FREE_ARG char*
213: #define FTOL 1.0e-10
214:
215: #define NRANSI
216: #define ITMAX 200
217:
218: #define TOL 2.0e-4
219:
220: #define CGOLD 0.3819660
221: #define ZEPS 1.0e-10
222: #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
223:
224: #define GOLD 1.618034
225: #define GLIMIT 100.0
226: #define TINY 1.0e-20
227:
228: static double maxarg1,maxarg2;
229: #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
230: #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
231:
232: #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
233: #define rint(a) floor(a+0.5)
234:
235: static double sqrarg;
236: #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
237: #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
238:
239: int imx;
240: int stepm;
241: /* Stepm, step in month: minimum step interpolation*/
242:
243: int estepm;
244: /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
245:
246: int m,nb;
1.85 brouard 247: long *num;
248: int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;
1.53 brouard 249: double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
1.55 lievre 250: double **pmmij, ***probs;
1.53 brouard 251: double dateintmean=0;
252:
253: double *weight;
254: int **s; /* Status */
255: double *agedc, **covar, idx;
256: int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
257:
258: double ftol=FTOL; /* Tolerance for computing Max Likelihood */
259: double ftolhess; /* Tolerance for computing hessian */
260:
261: /**************** split *************************/
262: static int split( char *path, char *dirc, char *name, char *ext, char *finame )
263: {
1.59 brouard 264: char *ss; /* pointer */
265: int l1, l2; /* length counters */
1.53 brouard 266:
1.59 brouard 267: l1 = strlen(path ); /* length of path */
268: if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
269: ss= strrchr( path, DIRSEPARATOR ); /* find last / */
270: if ( ss == NULL ) { /* no directory, so use current */
271: /*if(strrchr(path, ODIRSEPARATOR )==NULL)
272: printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
1.74 brouard 273: /* get current working directory */
274: /* extern char* getcwd ( char *buf , int len);*/
1.59 brouard 275: if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
276: return( GLOCK_ERROR_GETCWD );
277: }
278: strcpy( name, path ); /* we've got it */
279: } else { /* strip direcotry from path */
280: ss++; /* after this, the filename */
281: l2 = strlen( ss ); /* length of filename */
282: if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
283: strcpy( name, ss ); /* save file name */
284: strncpy( dirc, path, l1 - l2 ); /* now the directory */
285: dirc[l1-l2] = 0; /* add zero */
286: }
287: l1 = strlen( dirc ); /* length of directory */
1.85 brouard 288: /*#ifdef windows
1.59 brouard 289: if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
1.53 brouard 290: #else
1.59 brouard 291: if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }
1.53 brouard 292: #endif
1.85 brouard 293: */
1.59 brouard 294: ss = strrchr( name, '.' ); /* find last / */
295: ss++;
296: strcpy(ext,ss); /* save extension */
297: l1= strlen( name);
298: l2= strlen(ss)+1;
299: strncpy( finame, name, l1-l2);
300: finame[l1-l2]= 0;
301: return( 0 ); /* we're done */
1.53 brouard 302: }
303:
304:
305: /******************************************/
306:
307: void replace(char *s, char*t)
308: {
309: int i;
310: int lg=20;
311: i=0;
312: lg=strlen(t);
313: for(i=0; i<= lg; i++) {
314: (s[i] = t[i]);
315: if (t[i]== '\\') s[i]='/';
316: }
317: }
318:
319: int nbocc(char *s, char occ)
320: {
321: int i,j=0;
322: int lg=20;
323: i=0;
324: lg=strlen(s);
325: for(i=0; i<= lg; i++) {
326: if (s[i] == occ ) j++;
327: }
328: return j;
329: }
330:
331: void cutv(char *u,char *v, char*t, char occ)
332: {
333: /* cuts string t into u and v where u is ended by char occ excluding it
334: and v is after occ excluding it too : ex cutv(u,v,"abcdef2ghi2j",2)
335: gives u="abcedf" and v="ghi2j" */
336: int i,lg,j,p=0;
337: i=0;
338: for(j=0; j<=strlen(t)-1; j++) {
339: if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
340: }
341:
342: lg=strlen(t);
343: for(j=0; j<p; j++) {
344: (u[j] = t[j]);
345: }
346: u[p]='\0';
347:
348: for(j=0; j<= lg; j++) {
349: if (j>=(p+1))(v[j-p-1] = t[j]);
350: }
351: }
352:
353: /********************** nrerror ********************/
354:
355: void nrerror(char error_text[])
356: {
357: fprintf(stderr,"ERREUR ...\n");
358: fprintf(stderr,"%s\n",error_text);
1.59 brouard 359: exit(EXIT_FAILURE);
1.53 brouard 360: }
361: /*********************** vector *******************/
362: double *vector(int nl, int nh)
363: {
364: double *v;
365: v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
366: if (!v) nrerror("allocation failure in vector");
367: return v-nl+NR_END;
368: }
369:
370: /************************ free vector ******************/
371: void free_vector(double*v, int nl, int nh)
372: {
373: free((FREE_ARG)(v+nl-NR_END));
374: }
375:
376: /************************ivector *******************************/
1.85 brouard 377: int *ivector(long nl,long nh)
1.76 brouard 378: {
1.85 brouard 379: int *v;
380: v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
381: if (!v) nrerror("allocation failure in ivector");
1.76 brouard 382: return v-nl+NR_END;
383: }
384:
385: /******************free ivector **************************/
1.85 brouard 386: void free_ivector(int *v, long nl, long nh)
1.76 brouard 387: {
388: free((FREE_ARG)(v+nl-NR_END));
389: }
390:
1.85 brouard 391: /************************lvector *******************************/
392: long *lvector(long nl,long nh)
1.53 brouard 393: {
1.85 brouard 394: long *v;
395: v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
1.53 brouard 396: if (!v) nrerror("allocation failure in ivector");
397: return v-nl+NR_END;
398: }
399:
1.85 brouard 400: /******************free lvector **************************/
401: void free_lvector(long *v, long nl, long nh)
1.53 brouard 402: {
403: free((FREE_ARG)(v+nl-NR_END));
404: }
405:
406: /******************* imatrix *******************************/
407: int **imatrix(long nrl, long nrh, long ncl, long nch)
408: /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
409: {
410: long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
411: int **m;
412:
413: /* allocate pointers to rows */
414: m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
415: if (!m) nrerror("allocation failure 1 in matrix()");
416: m += NR_END;
417: m -= nrl;
418:
419:
420: /* allocate rows and set pointers to them */
421: m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
422: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
423: m[nrl] += NR_END;
424: m[nrl] -= ncl;
425:
426: for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
427:
428: /* return pointer to array of pointers to rows */
429: return m;
430: }
431:
432: /****************** free_imatrix *************************/
433: void free_imatrix(m,nrl,nrh,ncl,nch)
434: int **m;
435: long nch,ncl,nrh,nrl;
436: /* free an int matrix allocated by imatrix() */
437: {
438: free((FREE_ARG) (m[nrl]+ncl-NR_END));
439: free((FREE_ARG) (m+nrl-NR_END));
440: }
441:
442: /******************* matrix *******************************/
443: double **matrix(long nrl, long nrh, long ncl, long nch)
444: {
445: long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
446: double **m;
447:
448: m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
449: if (!m) nrerror("allocation failure 1 in matrix()");
450: m += NR_END;
451: m -= nrl;
452:
453: m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
454: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
455: m[nrl] += NR_END;
456: m[nrl] -= ncl;
457:
458: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
459: return m;
1.85 brouard 460: /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1])
1.74 brouard 461: */
1.53 brouard 462: }
463:
464: /*************************free matrix ************************/
465: void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
466: {
467: free((FREE_ARG)(m[nrl]+ncl-NR_END));
468: free((FREE_ARG)(m+nrl-NR_END));
469: }
470:
471: /******************* ma3x *******************************/
472: double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
473: {
474: long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
475: double ***m;
476:
477: m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
478: if (!m) nrerror("allocation failure 1 in matrix()");
479: m += NR_END;
480: m -= nrl;
481:
482: m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
483: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
484: m[nrl] += NR_END;
485: m[nrl] -= ncl;
486:
487: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
488:
489: m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
490: if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
491: m[nrl][ncl] += NR_END;
492: m[nrl][ncl] -= nll;
493: for (j=ncl+1; j<=nch; j++)
494: m[nrl][j]=m[nrl][j-1]+nlay;
495:
496: for (i=nrl+1; i<=nrh; i++) {
497: m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
498: for (j=ncl+1; j<=nch; j++)
499: m[i][j]=m[i][j-1]+nlay;
500: }
1.74 brouard 501: return m;
502: /* gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
503: &(m[i][j][k]) <=> *((*(m+i) + j)+k)
504: */
1.53 brouard 505: }
506:
507: /*************************free ma3x ************************/
508: void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
509: {
510: free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
511: free((FREE_ARG)(m[nrl]+ncl-NR_END));
512: free((FREE_ARG)(m+nrl-NR_END));
513: }
514:
515: /***************** f1dim *************************/
516: extern int ncom;
517: extern double *pcom,*xicom;
518: extern double (*nrfunc)(double []);
519:
520: double f1dim(double x)
521: {
522: int j;
523: double f;
524: double *xt;
525:
526: xt=vector(1,ncom);
527: for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
528: f=(*nrfunc)(xt);
529: free_vector(xt,1,ncom);
530: return f;
531: }
532:
533: /*****************brent *************************/
534: double brent(double ax, double bx, double cx, double (*f)(double), double tol, double *xmin)
535: {
536: int iter;
537: double a,b,d,etemp;
538: double fu,fv,fw,fx;
539: double ftemp;
540: double p,q,r,tol1,tol2,u,v,w,x,xm;
541: double e=0.0;
542:
543: a=(ax < cx ? ax : cx);
544: b=(ax > cx ? ax : cx);
545: x=w=v=bx;
546: fw=fv=fx=(*f)(x);
547: for (iter=1;iter<=ITMAX;iter++) {
548: xm=0.5*(a+b);
549: tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
550: /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
551: printf(".");fflush(stdout);
552: fprintf(ficlog,".");fflush(ficlog);
553: #ifdef DEBUG
554: printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
555: fprintf(ficlog,"br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
556: /* if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
557: #endif
558: if (fabs(x-xm) <= (tol2-0.5*(b-a))){
559: *xmin=x;
560: return fx;
561: }
562: ftemp=fu;
563: if (fabs(e) > tol1) {
564: r=(x-w)*(fx-fv);
565: q=(x-v)*(fx-fw);
566: p=(x-v)*q-(x-w)*r;
567: q=2.0*(q-r);
568: if (q > 0.0) p = -p;
569: q=fabs(q);
570: etemp=e;
571: e=d;
572: if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
573: d=CGOLD*(e=(x >= xm ? a-x : b-x));
574: else {
575: d=p/q;
576: u=x+d;
577: if (u-a < tol2 || b-u < tol2)
578: d=SIGN(tol1,xm-x);
579: }
580: } else {
581: d=CGOLD*(e=(x >= xm ? a-x : b-x));
582: }
583: u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
584: fu=(*f)(u);
585: if (fu <= fx) {
586: if (u >= x) a=x; else b=x;
587: SHFT(v,w,x,u)
588: SHFT(fv,fw,fx,fu)
589: } else {
590: if (u < x) a=u; else b=u;
591: if (fu <= fw || w == x) {
592: v=w;
593: w=u;
594: fv=fw;
595: fw=fu;
596: } else if (fu <= fv || v == x || v == w) {
597: v=u;
598: fv=fu;
599: }
600: }
601: }
602: nrerror("Too many iterations in brent");
603: *xmin=x;
604: return fx;
605: }
606:
607: /****************** mnbrak ***********************/
608:
609: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
610: double (*func)(double))
611: {
612: double ulim,u,r,q, dum;
613: double fu;
614:
615: *fa=(*func)(*ax);
616: *fb=(*func)(*bx);
617: if (*fb > *fa) {
618: SHFT(dum,*ax,*bx,dum)
619: SHFT(dum,*fb,*fa,dum)
620: }
621: *cx=(*bx)+GOLD*(*bx-*ax);
622: *fc=(*func)(*cx);
623: while (*fb > *fc) {
624: r=(*bx-*ax)*(*fb-*fc);
625: q=(*bx-*cx)*(*fb-*fa);
626: u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
627: (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));
628: ulim=(*bx)+GLIMIT*(*cx-*bx);
629: if ((*bx-u)*(u-*cx) > 0.0) {
630: fu=(*func)(u);
631: } else if ((*cx-u)*(u-ulim) > 0.0) {
632: fu=(*func)(u);
633: if (fu < *fc) {
634: SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
635: SHFT(*fb,*fc,fu,(*func)(u))
636: }
637: } else if ((u-ulim)*(ulim-*cx) >= 0.0) {
638: u=ulim;
639: fu=(*func)(u);
640: } else {
641: u=(*cx)+GOLD*(*cx-*bx);
642: fu=(*func)(u);
643: }
644: SHFT(*ax,*bx,*cx,u)
645: SHFT(*fa,*fb,*fc,fu)
646: }
647: }
648:
649: /*************** linmin ************************/
650:
651: int ncom;
652: double *pcom,*xicom;
653: double (*nrfunc)(double []);
654:
655: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
656: {
657: double brent(double ax, double bx, double cx,
658: double (*f)(double), double tol, double *xmin);
659: double f1dim(double x);
660: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
661: double *fc, double (*func)(double));
662: int j;
663: double xx,xmin,bx,ax;
664: double fx,fb,fa;
665:
666: ncom=n;
667: pcom=vector(1,n);
668: xicom=vector(1,n);
669: nrfunc=func;
670: for (j=1;j<=n;j++) {
671: pcom[j]=p[j];
672: xicom[j]=xi[j];
673: }
674: ax=0.0;
675: xx=1.0;
676: mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);
677: *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);
678: #ifdef DEBUG
679: printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
680: fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
681: #endif
682: for (j=1;j<=n;j++) {
683: xi[j] *= xmin;
684: p[j] += xi[j];
685: }
686: free_vector(xicom,1,n);
687: free_vector(pcom,1,n);
688: }
689:
690: /*************** powell ************************/
691: void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
692: double (*func)(double []))
693: {
694: void linmin(double p[], double xi[], int n, double *fret,
695: double (*func)(double []));
696: int i,ibig,j;
697: double del,t,*pt,*ptt,*xit;
698: double fp,fptt;
699: double *xits;
700: pt=vector(1,n);
701: ptt=vector(1,n);
702: xit=vector(1,n);
703: xits=vector(1,n);
704: *fret=(*func)(p);
705: for (j=1;j<=n;j++) pt[j]=p[j];
706: for (*iter=1;;++(*iter)) {
707: fp=(*fret);
708: ibig=0;
709: del=0.0;
710: printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
711: fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
1.76 brouard 712: fprintf(ficrespow,"%d %.12f",*iter,*fret);
713: for (i=1;i<=n;i++) {
1.53 brouard 714: printf(" %d %.12f",i, p[i]);
1.76 brouard 715: fprintf(ficlog," %d %.12lf",i, p[i]);
716: fprintf(ficrespow," %.12lf", p[i]);
717: }
1.53 brouard 718: printf("\n");
719: fprintf(ficlog,"\n");
1.76 brouard 720: fprintf(ficrespow,"\n");
1.53 brouard 721: for (i=1;i<=n;i++) {
722: for (j=1;j<=n;j++) xit[j]=xi[j][i];
723: fptt=(*fret);
724: #ifdef DEBUG
725: printf("fret=%lf \n",*fret);
726: fprintf(ficlog,"fret=%lf \n",*fret);
727: #endif
728: printf("%d",i);fflush(stdout);
729: fprintf(ficlog,"%d",i);fflush(ficlog);
730: linmin(p,xit,n,fret,func);
731: if (fabs(fptt-(*fret)) > del) {
732: del=fabs(fptt-(*fret));
733: ibig=i;
734: }
735: #ifdef DEBUG
736: printf("%d %.12e",i,(*fret));
737: fprintf(ficlog,"%d %.12e",i,(*fret));
738: for (j=1;j<=n;j++) {
739: xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
740: printf(" x(%d)=%.12e",j,xit[j]);
741: fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
742: }
743: for(j=1;j<=n;j++) {
744: printf(" p=%.12e",p[j]);
745: fprintf(ficlog," p=%.12e",p[j]);
746: }
747: printf("\n");
748: fprintf(ficlog,"\n");
749: #endif
750: }
751: if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
752: #ifdef DEBUG
753: int k[2],l;
754: k[0]=1;
755: k[1]=-1;
756: printf("Max: %.12e",(*func)(p));
757: fprintf(ficlog,"Max: %.12e",(*func)(p));
758: for (j=1;j<=n;j++) {
759: printf(" %.12e",p[j]);
760: fprintf(ficlog," %.12e",p[j]);
761: }
762: printf("\n");
763: fprintf(ficlog,"\n");
764: for(l=0;l<=1;l++) {
765: for (j=1;j<=n;j++) {
766: ptt[j]=p[j]+(p[j]-pt[j])*k[l];
767: printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
768: fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
769: }
770: printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
771: fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
772: }
773: #endif
774:
775:
776: free_vector(xit,1,n);
777: free_vector(xits,1,n);
778: free_vector(ptt,1,n);
779: free_vector(pt,1,n);
780: return;
781: }
782: if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
783: for (j=1;j<=n;j++) {
784: ptt[j]=2.0*p[j]-pt[j];
785: xit[j]=p[j]-pt[j];
786: pt[j]=p[j];
787: }
788: fptt=(*func)(ptt);
789: if (fptt < fp) {
790: t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);
791: if (t < 0.0) {
792: linmin(p,xit,n,fret,func);
793: for (j=1;j<=n;j++) {
794: xi[j][ibig]=xi[j][n];
795: xi[j][n]=xit[j];
796: }
797: #ifdef DEBUG
798: printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
799: fprintf(ficlog,"Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
800: for(j=1;j<=n;j++){
801: printf(" %.12e",xit[j]);
802: fprintf(ficlog," %.12e",xit[j]);
803: }
804: printf("\n");
805: fprintf(ficlog,"\n");
806: #endif
1.54 brouard 807: }
1.53 brouard 808: }
809: }
810: }
811:
1.54 brouard 812: /**** Prevalence limit (stable prevalence) ****************/
1.53 brouard 813:
814: double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
815: {
816: /* Computes the prevalence limit in each live state at age x by left multiplying the unit
817: matrix by transitions matrix until convergence is reached */
818:
819: int i, ii,j,k;
820: double min, max, maxmin, maxmax,sumnew=0.;
821: double **matprod2();
822: double **out, cov[NCOVMAX], **pmij();
823: double **newm;
824: double agefin, delaymax=50 ; /* Max number of years to converge */
825:
826: for (ii=1;ii<=nlstate+ndeath;ii++)
827: for (j=1;j<=nlstate+ndeath;j++){
828: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
829: }
830:
831: cov[1]=1.;
832:
833: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
834: for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
835: newm=savm;
836: /* Covariates have to be included here again */
837: cov[2]=agefin;
838:
839: for (k=1; k<=cptcovn;k++) {
840: cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
841: /* printf("ij=%d k=%d Tvar[k]=%d nbcode=%d cov=%lf codtab[ij][Tvar[k]]=%d \n",ij,k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], codtab[ij][Tvar[k]]);*/
842: }
843: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
844: for (k=1; k<=cptcovprod;k++)
845: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
846:
847: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
848: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
849: /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
850: out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
851:
852: savm=oldm;
853: oldm=newm;
854: maxmax=0.;
855: for(j=1;j<=nlstate;j++){
856: min=1.;
857: max=0.;
858: for(i=1; i<=nlstate; i++) {
859: sumnew=0;
860: for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
861: prlim[i][j]= newm[i][j]/(1-sumnew);
862: max=FMAX(max,prlim[i][j]);
863: min=FMIN(min,prlim[i][j]);
864: }
865: maxmin=max-min;
866: maxmax=FMAX(maxmax,maxmin);
867: }
868: if(maxmax < ftolpl){
869: return prlim;
870: }
871: }
872: }
873:
874: /*************** transition probabilities ***************/
875:
876: double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
877: {
878: double s1, s2;
879: /*double t34;*/
880: int i,j,j1, nc, ii, jj;
881:
882: for(i=1; i<= nlstate; i++){
883: for(j=1; j<i;j++){
884: for (nc=1, s2=0.;nc <=ncovmodel; nc++){
885: /*s2 += param[i][j][nc]*cov[nc];*/
886: s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
887: /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/
888: }
889: ps[i][j]=s2;
890: /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/
891: }
892: for(j=i+1; j<=nlstate+ndeath;j++){
893: for (nc=1, s2=0.;nc <=ncovmodel; nc++){
894: s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
895: /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/
896: }
897: ps[i][j]=s2;
898: }
899: }
900: /*ps[3][2]=1;*/
901:
902: for(i=1; i<= nlstate; i++){
903: s1=0;
904: for(j=1; j<i; j++)
905: s1+=exp(ps[i][j]);
906: for(j=i+1; j<=nlstate+ndeath; j++)
907: s1+=exp(ps[i][j]);
908: ps[i][i]=1./(s1+1.);
909: for(j=1; j<i; j++)
910: ps[i][j]= exp(ps[i][j])*ps[i][i];
911: for(j=i+1; j<=nlstate+ndeath; j++)
912: ps[i][j]= exp(ps[i][j])*ps[i][i];
913: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
914: } /* end i */
915:
916: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
917: for(jj=1; jj<= nlstate+ndeath; jj++){
918: ps[ii][jj]=0;
919: ps[ii][ii]=1;
920: }
921: }
922:
923:
924: /* for(ii=1; ii<= nlstate+ndeath; ii++){
925: for(jj=1; jj<= nlstate+ndeath; jj++){
926: printf("%lf ",ps[ii][jj]);
927: }
928: printf("\n ");
929: }
930: printf("\n ");printf("%lf ",cov[2]);*/
931: /*
932: for(i=1; i<= npar; i++) printf("%f ",x[i]);
933: goto end;*/
934: return ps;
935: }
936:
937: /**************** Product of 2 matrices ******************/
938:
939: double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
940: {
941: /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
942: b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
943: /* in, b, out are matrice of pointers which should have been initialized
944: before: only the contents of out is modified. The function returns
945: a pointer to pointers identical to out */
946: long i, j, k;
947: for(i=nrl; i<= nrh; i++)
948: for(k=ncolol; k<=ncoloh; k++)
949: for(j=ncl,out[i][k]=0.; j<=nch; j++)
950: out[i][k] +=in[i][j]*b[j][k];
951:
952: return out;
953: }
954:
955:
956: /************* Higher Matrix Product ***************/
957:
958: double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
959: {
1.66 brouard 960: /* Computes the transition matrix starting at age 'age' over
961: 'nhstepm*hstepm*stepm' months (i.e. until
962: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
963: nhstepm*hstepm matrices.
1.53 brouard 964: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
1.66 brouard 965: (typically every 2 years instead of every month which is too big
966: for the memory).
1.53 brouard 967: Model is determined by parameters x and covariates have to be
968: included manually here.
969:
970: */
971:
972: int i, j, d, h, k;
973: double **out, cov[NCOVMAX];
974: double **newm;
975:
976: /* Hstepm could be zero and should return the unit matrix */
977: for (i=1;i<=nlstate+ndeath;i++)
978: for (j=1;j<=nlstate+ndeath;j++){
979: oldm[i][j]=(i==j ? 1.0 : 0.0);
980: po[i][j][0]=(i==j ? 1.0 : 0.0);
981: }
982: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
983: for(h=1; h <=nhstepm; h++){
984: for(d=1; d <=hstepm; d++){
985: newm=savm;
986: /* Covariates have to be included here again */
987: cov[1]=1.;
988: cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
989: for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
990: for (k=1; k<=cptcovage;k++)
991: cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
992: for (k=1; k<=cptcovprod;k++)
993: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
994:
995:
996: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
997: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
998: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
999: pmij(pmmij,cov,ncovmodel,x,nlstate));
1000: savm=oldm;
1001: oldm=newm;
1002: }
1003: for(i=1; i<=nlstate+ndeath; i++)
1004: for(j=1;j<=nlstate+ndeath;j++) {
1005: po[i][j][h]=newm[i][j];
1006: /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
1007: */
1008: }
1009: } /* end h */
1010: return po;
1011: }
1012:
1013:
1014: /*************** log-likelihood *************/
1015: double func( double *x)
1016: {
1017: int i, ii, j, k, mi, d, kk;
1018: double l, ll[NLSTATEMAX], cov[NCOVMAX];
1019: double **out;
1020: double sw; /* Sum of weights */
1021: double lli; /* Individual log likelihood */
1.59 brouard 1022: int s1, s2;
1.68 lievre 1023: double bbh, survp;
1.53 brouard 1024: long ipmx;
1025: /*extern weight */
1026: /* We are differentiating ll according to initial status */
1027: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
1028: /*for(i=1;i<imx;i++)
1029: printf(" %d\n",s[4][i]);
1030: */
1031: cov[1]=1.;
1032:
1033: for(k=1; k<=nlstate; k++) ll[k]=0.;
1.61 brouard 1034:
1035: if(mle==1){
1036: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1037: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1038: for(mi=1; mi<= wav[i]-1; mi++){
1039: for (ii=1;ii<=nlstate+ndeath;ii++)
1040: for (j=1;j<=nlstate+ndeath;j++){
1041: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1042: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1043: }
1044: for(d=0; d<dh[mi][i]; d++){
1045: newm=savm;
1046: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1047: for (kk=1; kk<=cptcovage;kk++) {
1048: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1049: }
1050: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1051: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1052: savm=oldm;
1053: oldm=newm;
1054: } /* end mult */
1.53 brouard 1055:
1.61 brouard 1056: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
1057: /* But now since version 0.9 we anticipate for bias and large stepm.
1058: * If stepm is larger than one month (smallest stepm) and if the exact delay
1059: * (in months) between two waves is not a multiple of stepm, we rounded to
1060: * the nearest (and in case of equal distance, to the lowest) interval but now
1061: * we keep into memory the bias bh[mi][i] and also the previous matrix product
1062: * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
1063: * probability in order to take into account the bias as a fraction of the way
1064: * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
1065: * -stepm/2 to stepm/2 .
1066: * For stepm=1 the results are the same as for previous versions of Imach.
1067: * For stepm > 1 the results are less biased than in previous versions.
1068: */
1069: s1=s[mw[mi][i]][i];
1070: s2=s[mw[mi+1][i]][i];
1.64 lievre 1071: bbh=(double)bh[mi][i]/(double)stepm;
1072: /* bias is positive if real duration
1073: * is higher than the multiple of stepm and negative otherwise.
1074: */
1075: /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
1.71 brouard 1076: if( s2 > nlstate){
1077: /* i.e. if s2 is a death state and if the date of death is known then the contribution
1078: to the likelihood is the probability to die between last step unit time and current
1079: step unit time, which is also the differences between probability to die before dh
1080: and probability to die before dh-stepm .
1081: In version up to 0.92 likelihood was computed
1082: as if date of death was unknown. Death was treated as any other
1083: health state: the date of the interview describes the actual state
1084: and not the date of a change in health state. The former idea was
1085: to consider that at each interview the state was recorded
1086: (healthy, disable or death) and IMaCh was corrected; but when we
1087: introduced the exact date of death then we should have modified
1088: the contribution of an exact death to the likelihood. This new
1089: contribution is smaller and very dependent of the step unit
1090: stepm. It is no more the probability to die between last interview
1091: and month of death but the probability to survive from last
1092: interview up to one month before death multiplied by the
1093: probability to die within a month. Thanks to Chris
1094: Jackson for correcting this bug. Former versions increased
1095: mortality artificially. The bad side is that we add another loop
1096: which slows down the processing. The difference can be up to 10%
1097: lower mortality.
1098: */
1099: lli=log(out[s1][s2] - savm[s1][s2]);
1100: }else{
1101: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
1102: /* lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2]));*/ /* linear interpolation */
1103: }
1.64 lievre 1104: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
1105: /*if(lli ==000.0)*/
1106: /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
1.71 brouard 1107: ipmx +=1;
1.64 lievre 1108: sw += weight[i];
1109: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1110: } /* end of wave */
1111: } /* end of individual */
1112: } else if(mle==2){
1113: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1114: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1115: for(mi=1; mi<= wav[i]-1; mi++){
1116: for (ii=1;ii<=nlstate+ndeath;ii++)
1117: for (j=1;j<=nlstate+ndeath;j++){
1118: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1119: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1120: }
1121: for(d=0; d<=dh[mi][i]; d++){
1122: newm=savm;
1123: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1124: for (kk=1; kk<=cptcovage;kk++) {
1125: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1126: }
1127: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1128: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1129: savm=oldm;
1130: oldm=newm;
1131: } /* end mult */
1132:
1133: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
1134: /* But now since version 0.9 we anticipate for bias and large stepm.
1135: * If stepm is larger than one month (smallest stepm) and if the exact delay
1136: * (in months) between two waves is not a multiple of stepm, we rounded to
1137: * the nearest (and in case of equal distance, to the lowest) interval but now
1138: * we keep into memory the bias bh[mi][i] and also the previous matrix product
1139: * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
1140: * probability in order to take into account the bias as a fraction of the way
1141: * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
1142: * -stepm/2 to stepm/2 .
1143: * For stepm=1 the results are the same as for previous versions of Imach.
1144: * For stepm > 1 the results are less biased than in previous versions.
1145: */
1146: s1=s[mw[mi][i]][i];
1147: s2=s[mw[mi+1][i]][i];
1148: bbh=(double)bh[mi][i]/(double)stepm;
1149: /* bias is positive if real duration
1150: * is higher than the multiple of stepm and negative otherwise.
1151: */
1.63 lievre 1152: lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
1.64 lievre 1153: /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
1154: /*lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.-+bh)*out[s1][s2])); */ /* exponential interpolation */
1155: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
1156: /*if(lli ==000.0)*/
1157: /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
1158: ipmx +=1;
1159: sw += weight[i];
1160: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1161: } /* end of wave */
1162: } /* end of individual */
1163: } else if(mle==3){ /* exponential inter-extrapolation */
1164: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1165: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1166: for(mi=1; mi<= wav[i]-1; mi++){
1167: for (ii=1;ii<=nlstate+ndeath;ii++)
1168: for (j=1;j<=nlstate+ndeath;j++){
1169: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1170: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1171: }
1172: for(d=0; d<dh[mi][i]; d++){
1173: newm=savm;
1174: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1175: for (kk=1; kk<=cptcovage;kk++) {
1176: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1177: }
1178: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1179: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1180: savm=oldm;
1181: oldm=newm;
1182: } /* end mult */
1183:
1184: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
1185: /* But now since version 0.9 we anticipate for bias and large stepm.
1186: * If stepm is larger than one month (smallest stepm) and if the exact delay
1187: * (in months) between two waves is not a multiple of stepm, we rounded to
1188: * the nearest (and in case of equal distance, to the lowest) interval but now
1189: * we keep into memory the bias bh[mi][i] and also the previous matrix product
1190: * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
1191: * probability in order to take into account the bias as a fraction of the way
1192: * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
1193: * -stepm/2 to stepm/2 .
1194: * For stepm=1 the results are the same as for previous versions of Imach.
1195: * For stepm > 1 the results are less biased than in previous versions.
1196: */
1197: s1=s[mw[mi][i]][i];
1198: s2=s[mw[mi+1][i]][i];
1199: bbh=(double)bh[mi][i]/(double)stepm;
1200: /* bias is positive if real duration
1201: * is higher than the multiple of stepm and negative otherwise.
1202: */
1203: /* lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); */ /* linear interpolation */
1204: lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
1.61 brouard 1205: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
1206: /*if(lli ==000.0)*/
1207: /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
1208: ipmx +=1;
1209: sw += weight[i];
1210: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1211: } /* end of wave */
1212: } /* end of individual */
1.84 brouard 1213: }else if (mle==4){ /* ml=4 no inter-extrapolation */
1.61 brouard 1214: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1215: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1216: for(mi=1; mi<= wav[i]-1; mi++){
1217: for (ii=1;ii<=nlstate+ndeath;ii++)
1218: for (j=1;j<=nlstate+ndeath;j++){
1219: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1220: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1221: }
1222: for(d=0; d<dh[mi][i]; d++){
1223: newm=savm;
1224: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1225: for (kk=1; kk<=cptcovage;kk++) {
1226: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1227: }
1228:
1229: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1230: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1231: savm=oldm;
1232: oldm=newm;
1233: } /* end mult */
1234:
1.84 brouard 1235: s1=s[mw[mi][i]][i];
1236: s2=s[mw[mi+1][i]][i];
1237: if( s2 > nlstate){
1238: lli=log(out[s1][s2] - savm[s1][s2]);
1239: }else{
1240: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
1241: }
1242: ipmx +=1;
1243: sw += weight[i];
1244: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1.85 brouard 1245: /* printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
1.84 brouard 1246: } /* end of wave */
1247: } /* end of individual */
1248: }else{ /* ml=5 no inter-extrapolation no jackson =0.8a */
1249: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1250: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1251: for(mi=1; mi<= wav[i]-1; mi++){
1252: for (ii=1;ii<=nlstate+ndeath;ii++)
1253: for (j=1;j<=nlstate+ndeath;j++){
1254: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1255: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1256: }
1257: for(d=0; d<dh[mi][i]; d++){
1258: newm=savm;
1259: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1260: for (kk=1; kk<=cptcovage;kk++) {
1261: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1262: }
1263:
1264: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1265: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1266: savm=oldm;
1267: oldm=newm;
1268: } /* end mult */
1269:
1270: s1=s[mw[mi][i]][i];
1271: s2=s[mw[mi+1][i]][i];
1.61 brouard 1272: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
1273: ipmx +=1;
1274: sw += weight[i];
1275: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1.84 brouard 1276: /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]);*/
1.61 brouard 1277: } /* end of wave */
1278: } /* end of individual */
1279: } /* End of if */
1.53 brouard 1280: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
1281: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
1282: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
1.85 brouard 1283: return -l;
1284: }
1285:
1286: /*************** log-likelihood *************/
1287: double funcone( double *x)
1288: {
1289: int i, ii, j, k, mi, d, kk;
1290: double l, ll[NLSTATEMAX], cov[NCOVMAX];
1291: double **out;
1292: double lli; /* Individual log likelihood */
1293: int s1, s2;
1294: double bbh, survp;
1295: /*extern weight */
1296: /* We are differentiating ll according to initial status */
1297: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
1298: /*for(i=1;i<imx;i++)
1299: printf(" %d\n",s[4][i]);
1300: */
1301: cov[1]=1.;
1302:
1303: for(k=1; k<=nlstate; k++) ll[k]=0.;
1304:
1305: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1306: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1307: for(mi=1; mi<= wav[i]-1; mi++){
1308: for (ii=1;ii<=nlstate+ndeath;ii++)
1309: for (j=1;j<=nlstate+ndeath;j++){
1310: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1311: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1312: }
1313: for(d=0; d<dh[mi][i]; d++){
1314: newm=savm;
1315: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1316: for (kk=1; kk<=cptcovage;kk++) {
1317: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1318: }
1319: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1320: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1321: savm=oldm;
1322: oldm=newm;
1323: } /* end mult */
1324:
1325: s1=s[mw[mi][i]][i];
1326: s2=s[mw[mi+1][i]][i];
1327: bbh=(double)bh[mi][i]/(double)stepm;
1328: /* bias is positive if real duration
1329: * is higher than the multiple of stepm and negative otherwise.
1330: */
1331: if( s2 > nlstate && (mle <5) ){ /* Jackson */
1332: lli=log(out[s1][s2] - savm[s1][s2]);
1333: } else if (mle==1){
1334: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
1335: } else if(mle==2){
1336: lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
1337: } else if(mle==3){ /* exponential inter-extrapolation */
1338: lli= (savm[s1][s2]>(double)1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
1339: } else if (mle==4){ /* mle=4 no inter-extrapolation */
1340: lli=log(out[s1][s2]); /* Original formula */
1341: } else{ /* ml>=5 no inter-extrapolation no jackson =0.8a */
1342: lli=log(out[s1][s2]); /* Original formula */
1343: } /* End of if */
1344: ipmx +=1;
1345: sw += weight[i];
1346: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1347: /* printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
1348: if(globpr){
1.86 ! brouard 1349: fprintf(ficresilk,"%ld %6d %1d %1d %1d %1d %3d %10.6f %6.4f\
! 1350: %10.6f %10.6f %10.6f ", \
! 1351: num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
! 1352: 2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
1.85 brouard 1353: for(k=1,l=0.; k<=nlstate; k++)
1354: fprintf(ficresilk," %10.6f",ll[k]);
1355: fprintf(ficresilk,"\n");
1356: }
1357: } /* end of wave */
1358: } /* end of individual */
1359: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
1360: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
1361: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
1.53 brouard 1362: return -l;
1363: }
1364:
1365:
1.85 brouard 1366: void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpr, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
1367: {
1368: /* This routine should help understanding what is done with the selection of individuals/waves and
1369: to check the exact contribution to the likelihood.
1370: Plotting could be done.
1371: */
1372: int k;
1373: if(globpr !=0){ /* Just counts and sums no printings */
1374: strcpy(fileresilk,"ilk");
1375: strcat(fileresilk,fileres);
1376: if((ficresilk=fopen(fileresilk,"w"))==NULL) {
1377: printf("Problem with resultfile: %s\n", fileresilk);
1378: fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
1379: }
1.86 ! brouard 1380: fprintf(ficresilk, "#individual(line's record) s1 s2 wave# effective_wave# number_of_product_matrix pij weight 2ln(pij)*weight 0pij_x 0pij_(x-stepm) cumulating_loglikeli_by_health_state\n");
! 1381: fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight out sav ");
1.85 brouard 1382: /* i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
1383: for(k=1; k<=nlstate; k++)
1384: fprintf(ficresilk," ll[%d]",k);
1385: fprintf(ficresilk,"\n");
1386: }
1387:
1388: *fretone=(*funcone)(p);
1.86 ! brouard 1389: if(globpr !=0){
1.85 brouard 1390: fclose(ficresilk);
1.86 ! brouard 1391: if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
! 1392: printf("Problem with html file: %s\n", optionfilehtm);
! 1393: fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
! 1394: exit(0);
! 1395: }
! 1396: else{
! 1397: fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",fileresilk);
! 1398: fclose(fichtm);
! 1399: }
! 1400: }
1.85 brouard 1401: return;
1402: }
1403:
1.53 brouard 1404: /*********** Maximum Likelihood Estimation ***************/
1405:
1406: void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
1407: {
1408: int i,j, iter;
1.74 brouard 1409: double **xi;
1.53 brouard 1410: double fret;
1.85 brouard 1411: double fretone; /* Only one call to likelihood */
1.76 brouard 1412: char filerespow[FILENAMELENGTH];
1.53 brouard 1413: xi=matrix(1,npar,1,npar);
1414: for (i=1;i<=npar;i++)
1415: for (j=1;j<=npar;j++)
1416: xi[i][j]=(i==j ? 1.0 : 0.0);
1417: printf("Powell\n"); fprintf(ficlog,"Powell\n");
1.76 brouard 1418: strcpy(filerespow,"pow");
1419: strcat(filerespow,fileres);
1420: if((ficrespow=fopen(filerespow,"w"))==NULL) {
1421: printf("Problem with resultfile: %s\n", filerespow);
1422: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
1423: }
1424: fprintf(ficrespow,"# Powell\n# iter -2*LL");
1425: for (i=1;i<=nlstate;i++)
1426: for(j=1;j<=nlstate+ndeath;j++)
1427: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
1428: fprintf(ficrespow,"\n");
1.85 brouard 1429:
1.53 brouard 1430: powell(p,xi,npar,ftol,&iter,&fret,func);
1431:
1.76 brouard 1432: fclose(ficrespow);
1433: printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
1.65 lievre 1434: fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
1.53 brouard 1435: fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
1436:
1437: }
1438:
1439: /**** Computes Hessian and covariance matrix ***/
1440: void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
1441: {
1442: double **a,**y,*x,pd;
1443: double **hess;
1444: int i, j,jk;
1445: int *indx;
1446:
1447: double hessii(double p[], double delta, int theta, double delti[]);
1448: double hessij(double p[], double delti[], int i, int j);
1449: void lubksb(double **a, int npar, int *indx, double b[]) ;
1450: void ludcmp(double **a, int npar, int *indx, double *d) ;
1451:
1452: hess=matrix(1,npar,1,npar);
1453:
1454: printf("\nCalculation of the hessian matrix. Wait...\n");
1455: fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
1456: for (i=1;i<=npar;i++){
1457: printf("%d",i);fflush(stdout);
1458: fprintf(ficlog,"%d",i);fflush(ficlog);
1459: hess[i][i]=hessii(p,ftolhess,i,delti);
1460: /*printf(" %f ",p[i]);*/
1461: /*printf(" %lf ",hess[i][i]);*/
1462: }
1463:
1464: for (i=1;i<=npar;i++) {
1465: for (j=1;j<=npar;j++) {
1466: if (j>i) {
1467: printf(".%d%d",i,j);fflush(stdout);
1468: fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
1469: hess[i][j]=hessij(p,delti,i,j);
1470: hess[j][i]=hess[i][j];
1471: /*printf(" %lf ",hess[i][j]);*/
1472: }
1473: }
1474: }
1475: printf("\n");
1476: fprintf(ficlog,"\n");
1477:
1478: printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
1479: fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
1480:
1481: a=matrix(1,npar,1,npar);
1482: y=matrix(1,npar,1,npar);
1483: x=vector(1,npar);
1484: indx=ivector(1,npar);
1485: for (i=1;i<=npar;i++)
1486: for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
1487: ludcmp(a,npar,indx,&pd);
1488:
1489: for (j=1;j<=npar;j++) {
1490: for (i=1;i<=npar;i++) x[i]=0;
1491: x[j]=1;
1492: lubksb(a,npar,indx,x);
1493: for (i=1;i<=npar;i++){
1494: matcov[i][j]=x[i];
1495: }
1496: }
1497:
1498: printf("\n#Hessian matrix#\n");
1499: fprintf(ficlog,"\n#Hessian matrix#\n");
1500: for (i=1;i<=npar;i++) {
1501: for (j=1;j<=npar;j++) {
1502: printf("%.3e ",hess[i][j]);
1503: fprintf(ficlog,"%.3e ",hess[i][j]);
1504: }
1505: printf("\n");
1506: fprintf(ficlog,"\n");
1507: }
1508:
1509: /* Recompute Inverse */
1510: for (i=1;i<=npar;i++)
1511: for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
1512: ludcmp(a,npar,indx,&pd);
1513:
1514: /* printf("\n#Hessian matrix recomputed#\n");
1515:
1516: for (j=1;j<=npar;j++) {
1517: for (i=1;i<=npar;i++) x[i]=0;
1518: x[j]=1;
1519: lubksb(a,npar,indx,x);
1520: for (i=1;i<=npar;i++){
1521: y[i][j]=x[i];
1522: printf("%.3e ",y[i][j]);
1523: fprintf(ficlog,"%.3e ",y[i][j]);
1524: }
1525: printf("\n");
1526: fprintf(ficlog,"\n");
1527: }
1528: */
1529:
1530: free_matrix(a,1,npar,1,npar);
1531: free_matrix(y,1,npar,1,npar);
1532: free_vector(x,1,npar);
1533: free_ivector(indx,1,npar);
1534: free_matrix(hess,1,npar,1,npar);
1535:
1536:
1537: }
1538:
1539: /*************** hessian matrix ****************/
1540: double hessii( double x[], double delta, int theta, double delti[])
1541: {
1542: int i;
1543: int l=1, lmax=20;
1544: double k1,k2;
1545: double p2[NPARMAX+1];
1546: double res;
1547: double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;
1548: double fx;
1549: int k=0,kmax=10;
1550: double l1;
1551:
1552: fx=func(x);
1553: for (i=1;i<=npar;i++) p2[i]=x[i];
1554: for(l=0 ; l <=lmax; l++){
1555: l1=pow(10,l);
1556: delts=delt;
1557: for(k=1 ; k <kmax; k=k+1){
1558: delt = delta*(l1*k);
1559: p2[theta]=x[theta] +delt;
1560: k1=func(p2)-fx;
1561: p2[theta]=x[theta]-delt;
1562: k2=func(p2)-fx;
1563: /*res= (k1-2.0*fx+k2)/delt/delt; */
1564: res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
1565:
1566: #ifdef DEBUG
1567: printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
1568: fprintf(ficlog,"%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
1569: #endif
1570: /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
1571: if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
1572: k=kmax;
1573: }
1574: else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
1575: k=kmax; l=lmax*10.;
1576: }
1577: else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
1578: delts=delt;
1579: }
1580: }
1581: }
1582: delti[theta]=delts;
1583: return res;
1584:
1585: }
1586:
1587: double hessij( double x[], double delti[], int thetai,int thetaj)
1588: {
1589: int i;
1590: int l=1, l1, lmax=20;
1591: double k1,k2,k3,k4,res,fx;
1592: double p2[NPARMAX+1];
1593: int k;
1594:
1595: fx=func(x);
1596: for (k=1; k<=2; k++) {
1597: for (i=1;i<=npar;i++) p2[i]=x[i];
1598: p2[thetai]=x[thetai]+delti[thetai]/k;
1599: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
1600: k1=func(p2)-fx;
1601:
1602: p2[thetai]=x[thetai]+delti[thetai]/k;
1603: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
1604: k2=func(p2)-fx;
1605:
1606: p2[thetai]=x[thetai]-delti[thetai]/k;
1607: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
1608: k3=func(p2)-fx;
1609:
1610: p2[thetai]=x[thetai]-delti[thetai]/k;
1611: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
1612: k4=func(p2)-fx;
1613: res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
1614: #ifdef DEBUG
1615: printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
1616: fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
1617: #endif
1618: }
1619: return res;
1620: }
1621:
1622: /************** Inverse of matrix **************/
1623: void ludcmp(double **a, int n, int *indx, double *d)
1624: {
1625: int i,imax,j,k;
1626: double big,dum,sum,temp;
1627: double *vv;
1628:
1629: vv=vector(1,n);
1630: *d=1.0;
1631: for (i=1;i<=n;i++) {
1632: big=0.0;
1633: for (j=1;j<=n;j++)
1634: if ((temp=fabs(a[i][j])) > big) big=temp;
1635: if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
1636: vv[i]=1.0/big;
1637: }
1638: for (j=1;j<=n;j++) {
1639: for (i=1;i<j;i++) {
1640: sum=a[i][j];
1641: for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
1642: a[i][j]=sum;
1643: }
1644: big=0.0;
1645: for (i=j;i<=n;i++) {
1646: sum=a[i][j];
1647: for (k=1;k<j;k++)
1648: sum -= a[i][k]*a[k][j];
1649: a[i][j]=sum;
1650: if ( (dum=vv[i]*fabs(sum)) >= big) {
1651: big=dum;
1652: imax=i;
1653: }
1654: }
1655: if (j != imax) {
1656: for (k=1;k<=n;k++) {
1657: dum=a[imax][k];
1658: a[imax][k]=a[j][k];
1659: a[j][k]=dum;
1660: }
1661: *d = -(*d);
1662: vv[imax]=vv[j];
1663: }
1664: indx[j]=imax;
1665: if (a[j][j] == 0.0) a[j][j]=TINY;
1666: if (j != n) {
1667: dum=1.0/(a[j][j]);
1668: for (i=j+1;i<=n;i++) a[i][j] *= dum;
1669: }
1670: }
1671: free_vector(vv,1,n); /* Doesn't work */
1672: ;
1673: }
1674:
1675: void lubksb(double **a, int n, int *indx, double b[])
1676: {
1677: int i,ii=0,ip,j;
1678: double sum;
1679:
1680: for (i=1;i<=n;i++) {
1681: ip=indx[i];
1682: sum=b[ip];
1683: b[ip]=b[i];
1684: if (ii)
1685: for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
1686: else if (sum) ii=i;
1687: b[i]=sum;
1688: }
1689: for (i=n;i>=1;i--) {
1690: sum=b[i];
1691: for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
1692: b[i]=sum/a[i][i];
1693: }
1694: }
1695:
1696: /************ Frequencies ********************/
1.84 brouard 1697: void freqsummary(char fileres[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, int *Tvaraff, int **nbcode, int *ncodemax,double **mint,double **anint)
1.53 brouard 1698: { /* Some frequencies */
1699:
1700: int i, m, jk, k1,i1, j1, bool, z1,z2,j;
1701: int first;
1702: double ***freq; /* Frequencies */
1.73 lievre 1703: double *pp, **prop;
1704: double pos,posprop, k2, dateintsum=0,k2cpt=0;
1.53 brouard 1705: FILE *ficresp;
1706: char fileresp[FILENAMELENGTH];
1707:
1708: pp=vector(1,nlstate);
1.74 brouard 1709: prop=matrix(1,nlstate,iagemin,iagemax+3);
1.53 brouard 1710: strcpy(fileresp,"p");
1711: strcat(fileresp,fileres);
1712: if((ficresp=fopen(fileresp,"w"))==NULL) {
1713: printf("Problem with prevalence resultfile: %s\n", fileresp);
1714: fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
1715: exit(0);
1716: }
1.74 brouard 1717: freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);
1.53 brouard 1718: j1=0;
1719:
1720: j=cptcoveff;
1721: if (cptcovn<1) {j=1;ncodemax[1]=1;}
1722:
1723: first=1;
1724:
1725: for(k1=1; k1<=j;k1++){
1726: for(i1=1; i1<=ncodemax[k1];i1++){
1727: j1++;
1728: /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
1729: scanf("%d", i);*/
1730: for (i=-1; i<=nlstate+ndeath; i++)
1731: for (jk=-1; jk<=nlstate+ndeath; jk++)
1.74 brouard 1732: for(m=iagemin; m <= iagemax+3; m++)
1.53 brouard 1733: freq[i][jk][m]=0;
1.73 lievre 1734:
1735: for (i=1; i<=nlstate; i++)
1.74 brouard 1736: for(m=iagemin; m <= iagemax+3; m++)
1.73 lievre 1737: prop[i][m]=0;
1.53 brouard 1738:
1739: dateintsum=0;
1740: k2cpt=0;
1741: for (i=1; i<=imx; i++) {
1742: bool=1;
1743: if (cptcovn>0) {
1744: for (z1=1; z1<=cptcoveff; z1++)
1745: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
1746: bool=0;
1747: }
1.58 lievre 1748: if (bool==1){
1.53 brouard 1749: for(m=firstpass; m<=lastpass; m++){
1750: k2=anint[m][i]+(mint[m][i]/12.);
1.84 brouard 1751: /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
1.74 brouard 1752: if(agev[m][i]==0) agev[m][i]=iagemax+1;
1753: if(agev[m][i]==1) agev[m][i]=iagemax+2;
1.73 lievre 1754: if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
1.53 brouard 1755: if (m<lastpass) {
1756: freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
1.74 brouard 1757: freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
1.53 brouard 1758: }
1759:
1.74 brouard 1760: if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
1.53 brouard 1761: dateintsum=dateintsum+k2;
1762: k2cpt++;
1763: }
1.84 brouard 1764: /*}*/
1.53 brouard 1765: }
1766: }
1767: }
1768:
1.84 brouard 1769: /* fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
1.53 brouard 1770:
1771: if (cptcovn>0) {
1772: fprintf(ficresp, "\n#********** Variable ");
1773: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
1774: fprintf(ficresp, "**********\n#");
1775: }
1776: for(i=1; i<=nlstate;i++)
1777: fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
1778: fprintf(ficresp, "\n");
1779:
1.74 brouard 1780: for(i=iagemin; i <= iagemax+3; i++){
1781: if(i==iagemax+3){
1.53 brouard 1782: fprintf(ficlog,"Total");
1783: }else{
1784: if(first==1){
1785: first=0;
1786: printf("See log file for details...\n");
1787: }
1788: fprintf(ficlog,"Age %d", i);
1789: }
1790: for(jk=1; jk <=nlstate ; jk++){
1791: for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
1792: pp[jk] += freq[jk][m][i];
1793: }
1794: for(jk=1; jk <=nlstate ; jk++){
1795: for(m=-1, pos=0; m <=0 ; m++)
1796: pos += freq[jk][m][i];
1797: if(pp[jk]>=1.e-10){
1798: if(first==1){
1799: printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
1800: }
1801: fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
1802: }else{
1803: if(first==1)
1804: printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
1805: fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
1806: }
1807: }
1808:
1809: for(jk=1; jk <=nlstate ; jk++){
1810: for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
1811: pp[jk] += freq[jk][m][i];
1.73 lievre 1812: }
1813: for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
1814: pos += pp[jk];
1815: posprop += prop[jk][i];
1.53 brouard 1816: }
1817: for(jk=1; jk <=nlstate ; jk++){
1818: if(pos>=1.e-5){
1819: if(first==1)
1820: printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
1821: fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
1822: }else{
1823: if(first==1)
1824: printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
1825: fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
1826: }
1.74 brouard 1827: if( i <= iagemax){
1.53 brouard 1828: if(pos>=1.e-5){
1.73 lievre 1829: fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
1.84 brouard 1830: /*probs[i][jk][j1]= pp[jk]/pos;*/
1.53 brouard 1831: /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
1832: }
1833: else
1.73 lievre 1834: fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
1.53 brouard 1835: }
1836: }
1837:
1.69 brouard 1838: for(jk=-1; jk <=nlstate+ndeath; jk++)
1839: for(m=-1; m <=nlstate+ndeath; m++)
1.53 brouard 1840: if(freq[jk][m][i] !=0 ) {
1841: if(first==1)
1842: printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
1843: fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
1844: }
1.74 brouard 1845: if(i <= iagemax)
1.53 brouard 1846: fprintf(ficresp,"\n");
1847: if(first==1)
1848: printf("Others in log...\n");
1849: fprintf(ficlog,"\n");
1850: }
1851: }
1852: }
1853: dateintmean=dateintsum/k2cpt;
1854:
1855: fclose(ficresp);
1.74 brouard 1856: free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);
1.53 brouard 1857: free_vector(pp,1,nlstate);
1.74 brouard 1858: free_matrix(prop,1,nlstate,iagemin, iagemax+3);
1.53 brouard 1859: /* End of Freq */
1860: }
1861:
1862: /************ Prevalence ********************/
1.84 brouard 1863: void prevalence(double ***probs, double agemin, double agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, int firstpass, int lastpass)
1.69 brouard 1864: {
1865: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
1866: in each health status at the date of interview (if between dateprev1 and dateprev2).
1867: We still use firstpass and lastpass as another selection.
1868: */
1.53 brouard 1869:
1870: int i, m, jk, k1, i1, j1, bool, z1,z2,j;
1871: double ***freq; /* Frequencies */
1.73 lievre 1872: double *pp, **prop;
1873: double pos,posprop;
1.69 brouard 1874: double y2; /* in fractional years */
1.74 brouard 1875: int iagemin, iagemax;
1.53 brouard 1876:
1.74 brouard 1877: iagemin= (int) agemin;
1878: iagemax= (int) agemax;
1879: /*pp=vector(1,nlstate);*/
1880: prop=matrix(1,nlstate,iagemin,iagemax+3);
1881: /* freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
1.53 brouard 1882: j1=0;
1883:
1884: j=cptcoveff;
1885: if (cptcovn<1) {j=1;ncodemax[1]=1;}
1886:
1887: for(k1=1; k1<=j;k1++){
1888: for(i1=1; i1<=ncodemax[k1];i1++){
1889: j1++;
1890:
1.73 lievre 1891: for (i=1; i<=nlstate; i++)
1.74 brouard 1892: for(m=iagemin; m <= iagemax+3; m++)
1893: prop[i][m]=0.0;
1.53 brouard 1894:
1.69 brouard 1895: for (i=1; i<=imx; i++) { /* Each individual */
1.53 brouard 1896: bool=1;
1897: if (cptcovn>0) {
1898: for (z1=1; z1<=cptcoveff; z1++)
1899: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
1900: bool=0;
1901: }
1902: if (bool==1) {
1.69 brouard 1903: for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
1904: y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
1905: if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
1.74 brouard 1906: if(agev[m][i]==0) agev[m][i]=iagemax+1;
1907: if(agev[m][i]==1) agev[m][i]=iagemax+2;
1908: if((int)agev[m][i] <iagemin || (int)agev[m][i] >iagemax+3) printf("Error on individual =%d agev[m][i]=%f m=%d\n",i, agev[m][i],m);
1909: if (s[m][i]>0 && s[m][i]<=nlstate) {
1910: /*if(i>4620) printf(" i=%d m=%d s[m][i]=%d (int)agev[m][i]=%d weight[i]=%f prop=%f\n",i,m,s[m][i],(int)agev[m][m],weight[i],prop[s[m][i]][(int)agev[m][i]]);*/
1911: prop[s[m][i]][(int)agev[m][i]] += weight[i];
1912: prop[s[m][i]][iagemax+3] += weight[i];
1913: }
1.53 brouard 1914: }
1.69 brouard 1915: } /* end selection of waves */
1.53 brouard 1916: }
1917: }
1.74 brouard 1918: for(i=iagemin; i <= iagemax+3; i++){
1.53 brouard 1919:
1.74 brouard 1920: for(jk=1,posprop=0; jk <=nlstate ; jk++) {
1921: posprop += prop[jk][i];
1922: }
1923:
1924: for(jk=1; jk <=nlstate ; jk++){
1925: if( i <= iagemax){
1926: if(posprop>=1.e-5){
1927: probs[i][jk][j1]= prop[jk][i]/posprop;
1928: }
1929: }
1930: }/* end jk */
1931: }/* end i */
1.53 brouard 1932: } /* end i1 */
1933: } /* end k1 */
1934:
1.74 brouard 1935: /* free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
1936: /*free_vector(pp,1,nlstate);*/
1937: free_matrix(prop,1,nlstate, iagemin,iagemax+3);
1938: } /* End of prevalence */
1.53 brouard 1939:
1940: /************* Waves Concatenation ***************/
1941:
1.59 brouard 1942: void concatwav(int wav[], int **dh, int **bh, int **mw, int **s, double *agedc, double **agev, int firstpass, int lastpass, int imx, int nlstate, int stepm)
1.53 brouard 1943: {
1944: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
1945: Death is a valid wave (if date is known).
1946: mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i
1.59 brouard 1947: dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
1.53 brouard 1948: and mw[mi+1][i]. dh depends on stepm.
1949: */
1950:
1951: int i, mi, m;
1952: /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
1953: double sum=0., jmean=0.;*/
1954: int first;
1955: int j, k=0,jk, ju, jl;
1956: double sum=0.;
1957: first=0;
1958: jmin=1e+5;
1959: jmax=-1;
1960: jmean=0.;
1961: for(i=1; i<=imx; i++){
1962: mi=0;
1963: m=firstpass;
1964: while(s[m][i] <= nlstate){
1.69 brouard 1965: if(s[m][i]>=1)
1.53 brouard 1966: mw[++mi][i]=m;
1967: if(m >=lastpass)
1968: break;
1969: else
1970: m++;
1971: }/* end while */
1972: if (s[m][i] > nlstate){
1973: mi++; /* Death is another wave */
1974: /* if(mi==0) never been interviewed correctly before death */
1975: /* Only death is a correct wave */
1976: mw[mi][i]=m;
1977: }
1978:
1979: wav[i]=mi;
1980: if(mi==0){
1981: if(first==0){
1.85 brouard 1982: printf("Warning! None valid information for:%ld line=%d (skipped) and may be others, see log file\n",num[i],i);
1.53 brouard 1983: first=1;
1984: }
1985: if(first==1){
1.85 brouard 1986: fprintf(ficlog,"Warning! None valid information for:%ld line=%d (skipped)\n",num[i],i);
1.53 brouard 1987: }
1988: } /* end mi==0 */
1.77 brouard 1989: } /* End individuals */
1.53 brouard 1990:
1991: for(i=1; i<=imx; i++){
1992: for(mi=1; mi<wav[i];mi++){
1993: if (stepm <=0)
1994: dh[mi][i]=1;
1995: else{
1.77 brouard 1996: if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
1.53 brouard 1997: if (agedc[i] < 2*AGESUP) {
1.85 brouard 1998: j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
1999: if(j==0) j=1; /* Survives at least one month after exam */
2000: else if(j<0){
2001: printf("Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
2002: j=1; /* Careful Patch */
1.86 ! brouard 2003: printf(" We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview.\n You MUST fix the contradiction between dates.\n",stepm);
1.85 brouard 2004: printf("Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
2005: fprintf(ficlog," We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview.\n You MUST fix the contradiction between dates.\n",stepm);
2006: }
2007: k=k+1;
2008: if (j >= jmax) jmax=j;
2009: if (j <= jmin) jmin=j;
2010: sum=sum+j;
2011: /*if (j<0) printf("j=%d num=%d \n",j,i);*/
2012: /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
1.53 brouard 2013: }
2014: }
2015: else{
2016: j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
1.68 lievre 2017: /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
1.53 brouard 2018: k=k+1;
2019: if (j >= jmax) jmax=j;
2020: else if (j <= jmin)jmin=j;
2021: /* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
1.73 lievre 2022: /*printf("%d %lf %d %d %d\n", i,agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);*/
1.85 brouard 2023: if(j<0){
2024: printf("Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
2025: fprintf(ficlog,"Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
2026: }
1.53 brouard 2027: sum=sum+j;
2028: }
2029: jk= j/stepm;
2030: jl= j -jk*stepm;
2031: ju= j -(jk+1)*stepm;
1.85 brouard 2032: if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
1.64 lievre 2033: if(jl==0){
2034: dh[mi][i]=jk;
2035: bh[mi][i]=0;
2036: }else{ /* We want a negative bias in order to only have interpolation ie
2037: * at the price of an extra matrix product in likelihood */
2038: dh[mi][i]=jk+1;
2039: bh[mi][i]=ju;
2040: }
2041: }else{
2042: if(jl <= -ju){
2043: dh[mi][i]=jk;
2044: bh[mi][i]=jl; /* bias is positive if real duration
2045: * is higher than the multiple of stepm and negative otherwise.
2046: */
2047: }
2048: else{
2049: dh[mi][i]=jk+1;
2050: bh[mi][i]=ju;
2051: }
2052: if(dh[mi][i]==0){
2053: dh[mi][i]=1; /* At least one step */
2054: bh[mi][i]=ju; /* At least one step */
1.71 brouard 2055: /* printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d %d\n",bh[mi][i],ju,jl,dh[mi][i],jk,stepm,i);*/
1.64 lievre 2056: }
1.85 brouard 2057: } /* end if mle */
2058: }
1.64 lievre 2059: } /* end wave */
1.53 brouard 2060: }
2061: jmean=sum/k;
2062: printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
2063: fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
2064: }
2065:
2066: /*********** Tricode ****************************/
2067: void tricode(int *Tvar, int **nbcode, int imx)
2068: {
1.58 lievre 2069:
2070: int Ndum[20],ij=1, k, j, i, maxncov=19;
1.53 brouard 2071: int cptcode=0;
2072: cptcoveff=0;
2073:
1.58 lievre 2074: for (k=0; k<maxncov; k++) Ndum[k]=0;
1.53 brouard 2075: for (k=1; k<=7; k++) ncodemax[k]=0;
2076:
2077: for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
1.58 lievre 2078: for (i=1; i<=imx; i++) { /*reads the data file to get the maximum
2079: modality*/
2080: ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
2081: Ndum[ij]++; /*store the modality */
1.53 brouard 2082: /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
1.58 lievre 2083: if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable
2084: Tvar[j]. If V=sex and male is 0 and
2085: female is 1, then cptcode=1.*/
1.53 brouard 2086: }
2087:
2088: for (i=0; i<=cptcode; i++) {
1.58 lievre 2089: if(Ndum[i]!=0) ncodemax[j]++; /* Nomber of modalities of the j th covariates. In fact ncodemax[j]=2 (dichotom. variables) but it can be more */
1.53 brouard 2090: }
1.58 lievre 2091:
1.53 brouard 2092: ij=1;
2093: for (i=1; i<=ncodemax[j]; i++) {
1.58 lievre 2094: for (k=0; k<= maxncov; k++) {
1.53 brouard 2095: if (Ndum[k] != 0) {
2096: nbcode[Tvar[j]][ij]=k;
1.58 lievre 2097: /* store the modality in an array. k is a modality. If we have model=V1+V1*sex then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
1.53 brouard 2098:
2099: ij++;
2100: }
2101: if (ij > ncodemax[j]) break;
2102: }
2103: }
2104: }
2105:
1.58 lievre 2106: for (k=0; k< maxncov; k++) Ndum[k]=0;
1.53 brouard 2107:
1.58 lievre 2108: for (i=1; i<=ncovmodel-2; i++) {
2109: /* Listing of all covariables in staement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
1.53 brouard 2110: ij=Tvar[i];
1.58 lievre 2111: Ndum[ij]++;
1.53 brouard 2112: }
2113:
2114: ij=1;
1.58 lievre 2115: for (i=1; i<= maxncov; i++) {
1.53 brouard 2116: if((Ndum[i]!=0) && (i<=ncovcol)){
1.58 lievre 2117: Tvaraff[ij]=i; /*For printing */
1.53 brouard 2118: ij++;
2119: }
2120: }
2121:
1.58 lievre 2122: cptcoveff=ij-1; /*Number of simple covariates*/
1.53 brouard 2123: }
2124:
2125: /*********** Health Expectancies ****************/
2126:
2127: void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij, int estepm,double delti[],double **matcov )
2128:
2129: {
2130: /* Health expectancies */
2131: int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
2132: double age, agelim, hf;
2133: double ***p3mat,***varhe;
2134: double **dnewm,**doldm;
2135: double *xp;
2136: double **gp, **gm;
2137: double ***gradg, ***trgradg;
2138: int theta;
2139:
1.74 brouard 2140: varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
1.53 brouard 2141: xp=vector(1,npar);
1.74 brouard 2142: dnewm=matrix(1,nlstate*nlstate,1,npar);
2143: doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
1.53 brouard 2144:
2145: fprintf(ficreseij,"# Health expectancies\n");
2146: fprintf(ficreseij,"# Age");
2147: for(i=1; i<=nlstate;i++)
2148: for(j=1; j<=nlstate;j++)
2149: fprintf(ficreseij," %1d-%1d (SE)",i,j);
2150: fprintf(ficreseij,"\n");
2151:
2152: if(estepm < stepm){
2153: printf ("Problem %d lower than %d\n",estepm, stepm);
2154: }
2155: else hstepm=estepm;
2156: /* We compute the life expectancy from trapezoids spaced every estepm months
2157: * This is mainly to measure the difference between two models: for example
2158: * if stepm=24 months pijx are given only every 2 years and by summing them
2159: * we are calculating an estimate of the Life Expectancy assuming a linear
1.66 brouard 2160: * progression in between and thus overestimating or underestimating according
1.53 brouard 2161: * to the curvature of the survival function. If, for the same date, we
2162: * estimate the model with stepm=1 month, we can keep estepm to 24 months
2163: * to compare the new estimate of Life expectancy with the same linear
2164: * hypothesis. A more precise result, taking into account a more precise
2165: * curvature will be obtained if estepm is as small as stepm. */
2166:
2167: /* For example we decided to compute the life expectancy with the smallest unit */
2168: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
2169: nhstepm is the number of hstepm from age to agelim
2170: nstepm is the number of stepm from age to agelin.
2171: Look at hpijx to understand the reason of that which relies in memory size
2172: and note for a fixed period like estepm months */
2173: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
2174: survival function given by stepm (the optimization length). Unfortunately it
2175: means that if the survival funtion is printed only each two years of age and if
2176: you sum them up and add 1 year (area under the trapezoids) you won't get the same
2177: results. So we changed our mind and took the option of the best precision.
2178: */
2179: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
2180:
2181: agelim=AGESUP;
2182: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
2183: /* nhstepm age range expressed in number of stepm */
2184: nstepm=(int) rint((agelim-age)*YEARM/stepm);
2185: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
2186: /* if (stepm >= YEARM) hstepm=1;*/
2187: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
2188: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
1.74 brouard 2189: gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
2190: gp=matrix(0,nhstepm,1,nlstate*nlstate);
2191: gm=matrix(0,nhstepm,1,nlstate*nlstate);
1.53 brouard 2192:
2193: /* Computed by stepm unit matrices, product of hstepm matrices, stored
2194: in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
2195: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);
2196:
2197:
2198: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
2199:
2200: /* Computing Variances of health expectancies */
2201:
2202: for(theta=1; theta <=npar; theta++){
2203: for(i=1; i<=npar; i++){
2204: xp[i] = x[i] + (i==theta ?delti[theta]:0);
2205: }
2206: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
2207:
2208: cptj=0;
2209: for(j=1; j<= nlstate; j++){
2210: for(i=1; i<=nlstate; i++){
2211: cptj=cptj+1;
2212: for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
2213: gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
2214: }
2215: }
2216: }
2217:
2218:
2219: for(i=1; i<=npar; i++)
2220: xp[i] = x[i] - (i==theta ?delti[theta]:0);
2221: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
2222:
2223: cptj=0;
2224: for(j=1; j<= nlstate; j++){
2225: for(i=1;i<=nlstate;i++){
2226: cptj=cptj+1;
2227: for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
1.77 brouard 2228:
1.53 brouard 2229: gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
2230: }
2231: }
2232: }
1.74 brouard 2233: for(j=1; j<= nlstate*nlstate; j++)
1.53 brouard 2234: for(h=0; h<=nhstepm-1; h++){
2235: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
2236: }
2237: }
2238:
2239: /* End theta */
2240:
1.74 brouard 2241: trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
1.53 brouard 2242:
2243: for(h=0; h<=nhstepm-1; h++)
1.74 brouard 2244: for(j=1; j<=nlstate*nlstate;j++)
1.53 brouard 2245: for(theta=1; theta <=npar; theta++)
2246: trgradg[h][j][theta]=gradg[h][theta][j];
2247:
2248:
1.74 brouard 2249: for(i=1;i<=nlstate*nlstate;i++)
2250: for(j=1;j<=nlstate*nlstate;j++)
1.53 brouard 2251: varhe[i][j][(int)age] =0.;
2252:
2253: printf("%d|",(int)age);fflush(stdout);
2254: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
2255: for(h=0;h<=nhstepm-1;h++){
2256: for(k=0;k<=nhstepm-1;k++){
1.74 brouard 2257: matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
2258: matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
2259: for(i=1;i<=nlstate*nlstate;i++)
2260: for(j=1;j<=nlstate*nlstate;j++)
1.53 brouard 2261: varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
2262: }
2263: }
2264: /* Computing expectancies */
2265: for(i=1; i<=nlstate;i++)
2266: for(j=1; j<=nlstate;j++)
2267: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
2268: eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
2269:
2270: /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
2271:
2272: }
2273:
2274: fprintf(ficreseij,"%3.0f",age );
2275: cptj=0;
2276: for(i=1; i<=nlstate;i++)
2277: for(j=1; j<=nlstate;j++){
2278: cptj++;
2279: fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
2280: }
2281: fprintf(ficreseij,"\n");
2282:
1.74 brouard 2283: free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
2284: free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
2285: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
2286: free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
1.53 brouard 2287: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2288: }
2289: printf("\n");
2290: fprintf(ficlog,"\n");
2291:
2292: free_vector(xp,1,npar);
1.74 brouard 2293: free_matrix(dnewm,1,nlstate*nlstate,1,npar);
2294: free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
2295: free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
1.53 brouard 2296: }
2297:
2298: /************ Variance ******************/
2299: void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav)
2300: {
2301: /* Variance of health expectancies */
2302: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
2303: /* double **newm;*/
2304: double **dnewm,**doldm;
2305: double **dnewmp,**doldmp;
2306: int i, j, nhstepm, hstepm, h, nstepm ;
2307: int k, cptcode;
2308: double *xp;
2309: double **gp, **gm; /* for var eij */
2310: double ***gradg, ***trgradg; /*for var eij */
2311: double **gradgp, **trgradgp; /* for var p point j */
2312: double *gpp, *gmp; /* for var p point j */
2313: double **varppt; /* for var p point j nlstate to nlstate+ndeath */
2314: double ***p3mat;
2315: double age,agelim, hf;
2316: double ***mobaverage;
2317: int theta;
2318: char digit[4];
1.55 lievre 2319: char digitp[25];
1.53 brouard 2320:
2321: char fileresprobmorprev[FILENAMELENGTH];
2322:
1.55 lievre 2323: if(popbased==1){
1.58 lievre 2324: if(mobilav!=0)
1.55 lievre 2325: strcpy(digitp,"-populbased-mobilav-");
2326: else strcpy(digitp,"-populbased-nomobil-");
2327: }
2328: else
1.53 brouard 2329: strcpy(digitp,"-stablbased-");
1.56 lievre 2330:
1.54 brouard 2331: if (mobilav!=0) {
1.53 brouard 2332: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.54 brouard 2333: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
2334: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
2335: printf(" Error in movingaverage mobilav=%d\n",mobilav);
2336: }
1.53 brouard 2337: }
2338:
2339: strcpy(fileresprobmorprev,"prmorprev");
2340: sprintf(digit,"%-d",ij);
2341: /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
2342: strcat(fileresprobmorprev,digit); /* Tvar to be done */
2343: strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
2344: strcat(fileresprobmorprev,fileres);
2345: if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
2346: printf("Problem with resultfile: %s\n", fileresprobmorprev);
2347: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
2348: }
2349: printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
2350: fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
1.66 brouard 2351: fprintf(ficresprobmorprev,"# probabilities of dying before estepm=%d months for people of exact age and weighted probabilities w1*p1j+w2*p2j+... stand dev in()\n",estepm);
1.53 brouard 2352: fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
2353: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
2354: fprintf(ficresprobmorprev," p.%-d SE",j);
2355: for(i=1; i<=nlstate;i++)
2356: fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
2357: }
2358: fprintf(ficresprobmorprev,"\n");
2359: if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
2360: printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
2361: fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
2362: exit(0);
2363: }
2364: else{
2365: fprintf(ficgp,"\n# Routine varevsij");
2366: }
2367: if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
2368: printf("Problem with html file: %s\n", optionfilehtm);
2369: fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
2370: exit(0);
2371: }
2372: else{
1.67 brouard 2373: fprintf(fichtm,"\n<li><h4> Computing probabilities of dying over estepm months as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");
2374: fprintf(fichtm,"\n<br>%s <br>\n",digitp);
1.53 brouard 2375: }
2376: varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
2377:
2378: fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n# (weighted average of eij where weights are the stable prevalence in health states i\n");
2379: fprintf(ficresvij,"# Age");
2380: for(i=1; i<=nlstate;i++)
2381: for(j=1; j<=nlstate;j++)
2382: fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
2383: fprintf(ficresvij,"\n");
2384:
2385: xp=vector(1,npar);
2386: dnewm=matrix(1,nlstate,1,npar);
2387: doldm=matrix(1,nlstate,1,nlstate);
2388: dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
2389: doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
2390:
2391: gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
2392: gpp=vector(nlstate+1,nlstate+ndeath);
2393: gmp=vector(nlstate+1,nlstate+ndeath);
2394: trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
2395:
2396: if(estepm < stepm){
2397: printf ("Problem %d lower than %d\n",estepm, stepm);
2398: }
2399: else hstepm=estepm;
2400: /* For example we decided to compute the life expectancy with the smallest unit */
2401: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
2402: nhstepm is the number of hstepm from age to agelim
2403: nstepm is the number of stepm from age to agelin.
2404: Look at hpijx to understand the reason of that which relies in memory size
2405: and note for a fixed period like k years */
2406: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
2407: survival function given by stepm (the optimization length). Unfortunately it
1.66 brouard 2408: means that if the survival funtion is printed every two years of age and if
1.53 brouard 2409: you sum them up and add 1 year (area under the trapezoids) you won't get the same
2410: results. So we changed our mind and took the option of the best precision.
2411: */
2412: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
2413: agelim = AGESUP;
2414: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
2415: nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
2416: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
2417: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2418: gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
2419: gp=matrix(0,nhstepm,1,nlstate);
2420: gm=matrix(0,nhstepm,1,nlstate);
2421:
2422:
2423: for(theta=1; theta <=npar; theta++){
1.66 brouard 2424: for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
1.53 brouard 2425: xp[i] = x[i] + (i==theta ?delti[theta]:0);
2426: }
2427: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
2428: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2429:
2430: if (popbased==1) {
1.54 brouard 2431: if(mobilav ==0){
1.53 brouard 2432: for(i=1; i<=nlstate;i++)
2433: prlim[i][i]=probs[(int)age][i][ij];
1.54 brouard 2434: }else{ /* mobilav */
1.53 brouard 2435: for(i=1; i<=nlstate;i++)
2436: prlim[i][i]=mobaverage[(int)age][i][ij];
2437: }
2438: }
2439:
2440: for(j=1; j<= nlstate; j++){
2441: for(h=0; h<=nhstepm; h++){
2442: for(i=1, gp[h][j]=0.;i<=nlstate;i++)
2443: gp[h][j] += prlim[i][i]*p3mat[i][j][h];
2444: }
2445: }
1.66 brouard 2446: /* This for computing probability of death (h=1 means
2447: computed over hstepm matrices product = hstepm*stepm months)
2448: as a weighted average of prlim.
2449: */
1.69 brouard 2450: for(j=nlstate+1;j<=nlstate+ndeath;j++){
1.68 lievre 2451: for(i=1,gpp[j]=0.; i<= nlstate; i++)
1.53 brouard 2452: gpp[j] += prlim[i][i]*p3mat[i][j][1];
2453: }
1.66 brouard 2454: /* end probability of death */
1.53 brouard 2455:
1.66 brouard 2456: for(i=1; i<=npar; i++) /* Computes gradient x - delta */
1.53 brouard 2457: xp[i] = x[i] - (i==theta ?delti[theta]:0);
2458: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
2459: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2460:
2461: if (popbased==1) {
1.54 brouard 2462: if(mobilav ==0){
1.53 brouard 2463: for(i=1; i<=nlstate;i++)
2464: prlim[i][i]=probs[(int)age][i][ij];
1.54 brouard 2465: }else{ /* mobilav */
1.53 brouard 2466: for(i=1; i<=nlstate;i++)
2467: prlim[i][i]=mobaverage[(int)age][i][ij];
2468: }
2469: }
2470:
2471: for(j=1; j<= nlstate; j++){
2472: for(h=0; h<=nhstepm; h++){
2473: for(i=1, gm[h][j]=0.;i<=nlstate;i++)
2474: gm[h][j] += prlim[i][i]*p3mat[i][j][h];
2475: }
2476: }
1.66 brouard 2477: /* This for computing probability of death (h=1 means
2478: computed over hstepm matrices product = hstepm*stepm months)
2479: as a weighted average of prlim.
2480: */
1.69 brouard 2481: for(j=nlstate+1;j<=nlstate+ndeath;j++){
1.68 lievre 2482: for(i=1,gmp[j]=0.; i<= nlstate; i++)
2483: gmp[j] += prlim[i][i]*p3mat[i][j][1];
1.53 brouard 2484: }
1.66 brouard 2485: /* end probability of death */
1.53 brouard 2486:
2487: for(j=1; j<= nlstate; j++) /* vareij */
2488: for(h=0; h<=nhstepm; h++){
2489: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
2490: }
1.68 lievre 2491:
1.53 brouard 2492: for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
2493: gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
2494: }
2495:
2496: } /* End theta */
2497:
2498: trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
2499:
2500: for(h=0; h<=nhstepm; h++) /* veij */
2501: for(j=1; j<=nlstate;j++)
2502: for(theta=1; theta <=npar; theta++)
2503: trgradg[h][j][theta]=gradg[h][theta][j];
2504:
2505: for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
1.69 brouard 2506: for(theta=1; theta <=npar; theta++)
1.53 brouard 2507: trgradgp[j][theta]=gradgp[theta][j];
1.69 brouard 2508:
1.53 brouard 2509:
2510: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
2511: for(i=1;i<=nlstate;i++)
2512: for(j=1;j<=nlstate;j++)
2513: vareij[i][j][(int)age] =0.;
2514:
2515: for(h=0;h<=nhstepm;h++){
2516: for(k=0;k<=nhstepm;k++){
2517: matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
2518: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
2519: for(i=1;i<=nlstate;i++)
2520: for(j=1;j<=nlstate;j++)
2521: vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
2522: }
2523: }
1.70 brouard 2524:
1.53 brouard 2525: /* pptj */
2526: matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
2527: matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
1.70 brouard 2528: for(j=nlstate+1;j<=nlstate+ndeath;j++)
2529: for(i=nlstate+1;i<=nlstate+ndeath;i++)
1.53 brouard 2530: varppt[j][i]=doldmp[j][i];
2531: /* end ppptj */
1.66 brouard 2532: /* x centered again */
1.53 brouard 2533: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
2534: prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
2535:
2536: if (popbased==1) {
1.54 brouard 2537: if(mobilav ==0){
1.53 brouard 2538: for(i=1; i<=nlstate;i++)
2539: prlim[i][i]=probs[(int)age][i][ij];
1.54 brouard 2540: }else{ /* mobilav */
1.53 brouard 2541: for(i=1; i<=nlstate;i++)
2542: prlim[i][i]=mobaverage[(int)age][i][ij];
2543: }
2544: }
1.70 brouard 2545:
1.66 brouard 2546: /* This for computing probability of death (h=1 means
2547: computed over hstepm (estepm) matrices product = hstepm*stepm months)
2548: as a weighted average of prlim.
2549: */
1.68 lievre 2550: for(j=nlstate+1;j<=nlstate+ndeath;j++){
2551: for(i=1,gmp[j]=0.;i<= nlstate; i++)
1.53 brouard 2552: gmp[j] += prlim[i][i]*p3mat[i][j][1];
2553: }
1.66 brouard 2554: /* end probability of death */
1.53 brouard 2555:
2556: fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
2557: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
2558: fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
2559: for(i=1; i<=nlstate;i++){
2560: fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
2561: }
2562: }
2563: fprintf(ficresprobmorprev,"\n");
2564:
2565: fprintf(ficresvij,"%.0f ",age );
2566: for(i=1; i<=nlstate;i++)
2567: for(j=1; j<=nlstate;j++){
2568: fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
2569: }
2570: fprintf(ficresvij,"\n");
2571: free_matrix(gp,0,nhstepm,1,nlstate);
2572: free_matrix(gm,0,nhstepm,1,nlstate);
2573: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
2574: free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
2575: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2576: } /* End age */
2577: free_vector(gpp,nlstate+1,nlstate+ndeath);
2578: free_vector(gmp,nlstate+1,nlstate+ndeath);
2579: free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
2580: free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
2581: fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
2582: /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
2583: fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
1.67 brouard 2584: /* fprintf(ficgp,"\n plot \"%s\" u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
2585: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
2586: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
2587: fprintf(ficgp,"\n plot \"%s\" u 1:($3) not w l 1 ",fileresprobmorprev);
2588: fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",fileresprobmorprev);
2589: fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)) not w l 2 ",fileresprobmorprev);
1.53 brouard 2590: fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",fileresprobmorprev,fileresprobmorprev);
1.71 brouard 2591: fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"varmuptjgr%s%s%s.png\"> <br>\n", estepm,digitp,optionfilefiname,digit);
1.53 brouard 2592: /* fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,YEARM,digitp,digit);
2593: */
1.71 brouard 2594: fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit);
1.53 brouard 2595:
2596: free_vector(xp,1,npar);
2597: free_matrix(doldm,1,nlstate,1,nlstate);
2598: free_matrix(dnewm,1,nlstate,1,npar);
2599: free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
2600: free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
2601: free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
1.55 lievre 2602: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.53 brouard 2603: fclose(ficresprobmorprev);
2604: fclose(ficgp);
2605: fclose(fichtm);
1.84 brouard 2606: } /* end varevsij */
1.53 brouard 2607:
2608: /************ Variance of prevlim ******************/
2609: void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij)
2610: {
2611: /* Variance of prevalence limit */
1.59 brouard 2612: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
1.53 brouard 2613: double **newm;
2614: double **dnewm,**doldm;
2615: int i, j, nhstepm, hstepm;
2616: int k, cptcode;
2617: double *xp;
2618: double *gp, *gm;
2619: double **gradg, **trgradg;
2620: double age,agelim;
2621: int theta;
2622:
1.54 brouard 2623: fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");
1.53 brouard 2624: fprintf(ficresvpl,"# Age");
2625: for(i=1; i<=nlstate;i++)
2626: fprintf(ficresvpl," %1d-%1d",i,i);
2627: fprintf(ficresvpl,"\n");
2628:
2629: xp=vector(1,npar);
2630: dnewm=matrix(1,nlstate,1,npar);
2631: doldm=matrix(1,nlstate,1,nlstate);
2632:
2633: hstepm=1*YEARM; /* Every year of age */
2634: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
2635: agelim = AGESUP;
2636: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
2637: nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
2638: if (stepm >= YEARM) hstepm=1;
2639: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
2640: gradg=matrix(1,npar,1,nlstate);
2641: gp=vector(1,nlstate);
2642: gm=vector(1,nlstate);
2643:
2644: for(theta=1; theta <=npar; theta++){
2645: for(i=1; i<=npar; i++){ /* Computes gradient */
2646: xp[i] = x[i] + (i==theta ?delti[theta]:0);
2647: }
2648: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2649: for(i=1;i<=nlstate;i++)
2650: gp[i] = prlim[i][i];
2651:
2652: for(i=1; i<=npar; i++) /* Computes gradient */
2653: xp[i] = x[i] - (i==theta ?delti[theta]:0);
2654: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2655: for(i=1;i<=nlstate;i++)
2656: gm[i] = prlim[i][i];
2657:
2658: for(i=1;i<=nlstate;i++)
2659: gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
2660: } /* End theta */
2661:
2662: trgradg =matrix(1,nlstate,1,npar);
2663:
2664: for(j=1; j<=nlstate;j++)
2665: for(theta=1; theta <=npar; theta++)
2666: trgradg[j][theta]=gradg[theta][j];
2667:
2668: for(i=1;i<=nlstate;i++)
2669: varpl[i][(int)age] =0.;
2670: matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
2671: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
2672: for(i=1;i<=nlstate;i++)
2673: varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
2674:
2675: fprintf(ficresvpl,"%.0f ",age );
2676: for(i=1; i<=nlstate;i++)
2677: fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
2678: fprintf(ficresvpl,"\n");
2679: free_vector(gp,1,nlstate);
2680: free_vector(gm,1,nlstate);
2681: free_matrix(gradg,1,npar,1,nlstate);
2682: free_matrix(trgradg,1,nlstate,1,npar);
2683: } /* End age */
2684:
2685: free_vector(xp,1,npar);
2686: free_matrix(doldm,1,nlstate,1,npar);
2687: free_matrix(dnewm,1,nlstate,1,nlstate);
2688:
2689: }
2690:
2691: /************ Variance of one-step probabilities ******************/
2692: void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)
2693: {
2694: int i, j=0, i1, k1, l1, t, tj;
2695: int k2, l2, j1, z1;
2696: int k=0,l, cptcode;
2697: int first=1, first1;
2698: double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
2699: double **dnewm,**doldm;
2700: double *xp;
2701: double *gp, *gm;
2702: double **gradg, **trgradg;
2703: double **mu;
2704: double age,agelim, cov[NCOVMAX];
2705: double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
2706: int theta;
2707: char fileresprob[FILENAMELENGTH];
2708: char fileresprobcov[FILENAMELENGTH];
2709: char fileresprobcor[FILENAMELENGTH];
2710:
2711: double ***varpij;
2712:
2713: strcpy(fileresprob,"prob");
2714: strcat(fileresprob,fileres);
2715: if((ficresprob=fopen(fileresprob,"w"))==NULL) {
2716: printf("Problem with resultfile: %s\n", fileresprob);
2717: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
2718: }
2719: strcpy(fileresprobcov,"probcov");
2720: strcat(fileresprobcov,fileres);
2721: if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
2722: printf("Problem with resultfile: %s\n", fileresprobcov);
2723: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
2724: }
2725: strcpy(fileresprobcor,"probcor");
2726: strcat(fileresprobcor,fileres);
2727: if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
2728: printf("Problem with resultfile: %s\n", fileresprobcor);
2729: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
2730: }
2731: printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
2732: fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
2733: printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
2734: fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
2735: printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
2736: fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
2737:
2738: fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
2739: fprintf(ficresprob,"# Age");
2740: fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
2741: fprintf(ficresprobcov,"# Age");
2742: fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
2743: fprintf(ficresprobcov,"# Age");
2744:
2745:
2746: for(i=1; i<=nlstate;i++)
2747: for(j=1; j<=(nlstate+ndeath);j++){
2748: fprintf(ficresprob," p%1d-%1d (SE)",i,j);
2749: fprintf(ficresprobcov," p%1d-%1d ",i,j);
2750: fprintf(ficresprobcor," p%1d-%1d ",i,j);
2751: }
1.69 brouard 2752: /* fprintf(ficresprob,"\n");
1.53 brouard 2753: fprintf(ficresprobcov,"\n");
2754: fprintf(ficresprobcor,"\n");
1.69 brouard 2755: */
2756: xp=vector(1,npar);
1.53 brouard 2757: dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
2758: doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
2759: mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
2760: varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
2761: first=1;
2762: if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
2763: printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
2764: fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
2765: exit(0);
2766: }
2767: else{
2768: fprintf(ficgp,"\n# Routine varprob");
2769: }
2770: if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
2771: printf("Problem with html file: %s\n", optionfilehtm);
2772: fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
2773: exit(0);
2774: }
2775: else{
2776: fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
2777: fprintf(fichtm,"\n");
2778:
2779: fprintf(fichtm,"\n<li><h4> Computing matrix of variance-covariance of step probabilities</h4></li>\n");
2780: fprintf(fichtm,"\nWe have drawn ellipsoids of confidence around the p<inf>ij</inf>, p<inf>kl</inf> to understand the covariance between two incidences. They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
2781: fprintf(fichtm,"\n<br> We have drawn x'cov<sup>-1</sup>x = 4 where x is the column vector (pij,pkl). It means that if pij and pkl where uncorrelated the (2X2) matrix would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 standard deviations wide on each axis. <br> When both incidences are correlated we diagonalised the inverse of the covariance matrix and made the appropriate rotation.<br> \n");
2782:
2783: }
2784:
2785: cov[1]=1;
2786: tj=cptcoveff;
2787: if (cptcovn<1) {tj=1;ncodemax[1]=1;}
2788: j1=0;
2789: for(t=1; t<=tj;t++){
2790: for(i1=1; i1<=ncodemax[t];i1++){
2791: j1++;
2792: if (cptcovn>0) {
2793: fprintf(ficresprob, "\n#********** Variable ");
2794: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
1.69 brouard 2795: fprintf(ficresprob, "**********\n#\n");
1.53 brouard 2796: fprintf(ficresprobcov, "\n#********** Variable ");
2797: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
1.69 brouard 2798: fprintf(ficresprobcov, "**********\n#\n");
1.53 brouard 2799:
2800: fprintf(ficgp, "\n#********** Variable ");
1.69 brouard 2801: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2802: fprintf(ficgp, "**********\n#\n");
1.53 brouard 2803:
2804:
2805: fprintf(fichtm, "\n<hr size=\"2\" color=\"#EC5E5E\">********** Variable ");
2806: for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2807: fprintf(fichtm, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
2808:
2809: fprintf(ficresprobcor, "\n#********** Variable ");
2810: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
1.69 brouard 2811: fprintf(ficresprobcor, "**********\n#");
1.53 brouard 2812: }
2813:
2814: for (age=bage; age<=fage; age ++){
2815: cov[2]=age;
2816: for (k=1; k<=cptcovn;k++) {
2817: cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
2818: }
2819: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
2820: for (k=1; k<=cptcovprod;k++)
2821: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
2822:
2823: gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
2824: trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
2825: gp=vector(1,(nlstate)*(nlstate+ndeath));
2826: gm=vector(1,(nlstate)*(nlstate+ndeath));
2827:
2828: for(theta=1; theta <=npar; theta++){
2829: for(i=1; i<=npar; i++)
1.74 brouard 2830: xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
1.53 brouard 2831:
2832: pmij(pmmij,cov,ncovmodel,xp,nlstate);
2833:
2834: k=0;
2835: for(i=1; i<= (nlstate); i++){
2836: for(j=1; j<=(nlstate+ndeath);j++){
2837: k=k+1;
2838: gp[k]=pmmij[i][j];
2839: }
2840: }
2841:
2842: for(i=1; i<=npar; i++)
1.74 brouard 2843: xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
1.53 brouard 2844:
2845: pmij(pmmij,cov,ncovmodel,xp,nlstate);
2846: k=0;
2847: for(i=1; i<=(nlstate); i++){
2848: for(j=1; j<=(nlstate+ndeath);j++){
2849: k=k+1;
2850: gm[k]=pmmij[i][j];
2851: }
2852: }
2853:
2854: for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
1.74 brouard 2855: gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
1.53 brouard 2856: }
2857:
2858: for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
2859: for(theta=1; theta <=npar; theta++)
2860: trgradg[j][theta]=gradg[theta][j];
2861:
2862: matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
2863: matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
1.59 brouard 2864: free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
2865: free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
2866: free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
2867: free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
2868:
1.53 brouard 2869: pmij(pmmij,cov,ncovmodel,x,nlstate);
2870:
2871: k=0;
2872: for(i=1; i<=(nlstate); i++){
2873: for(j=1; j<=(nlstate+ndeath);j++){
2874: k=k+1;
2875: mu[k][(int) age]=pmmij[i][j];
2876: }
2877: }
2878: for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
2879: for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
2880: varpij[i][j][(int)age] = doldm[i][j];
2881:
2882: /*printf("\n%d ",(int)age);
1.59 brouard 2883: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
2884: printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
2885: fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
2886: }*/
1.53 brouard 2887:
2888: fprintf(ficresprob,"\n%d ",(int)age);
2889: fprintf(ficresprobcov,"\n%d ",(int)age);
2890: fprintf(ficresprobcor,"\n%d ",(int)age);
2891:
2892: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
2893: fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
2894: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
2895: fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
2896: fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
2897: }
2898: i=0;
2899: for (k=1; k<=(nlstate);k++){
2900: for (l=1; l<=(nlstate+ndeath);l++){
2901: i=i++;
2902: fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
2903: fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
2904: for (j=1; j<=i;j++){
2905: fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
2906: fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
2907: }
2908: }
2909: }/* end of loop for state */
2910: } /* end of loop for age */
2911:
2912: /* Confidence intervalle of pij */
2913: /*
1.59 brouard 2914: fprintf(ficgp,"\nset noparametric;unset label");
2915: fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
2916: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
2917: fprintf(fichtm,"\n<br>Probability with confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);
2918: fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
2919: fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
2920: fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
1.53 brouard 2921: */
2922:
2923: /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
2924: first1=1;
2925: for (k2=1; k2<=(nlstate);k2++){
2926: for (l2=1; l2<=(nlstate+ndeath);l2++){
2927: if(l2==k2) continue;
2928: j=(k2-1)*(nlstate+ndeath)+l2;
2929: for (k1=1; k1<=(nlstate);k1++){
2930: for (l1=1; l1<=(nlstate+ndeath);l1++){
2931: if(l1==k1) continue;
2932: i=(k1-1)*(nlstate+ndeath)+l1;
2933: if(i<=j) continue;
2934: for (age=bage; age<=fage; age ++){
2935: if ((int)age %5==0){
2936: v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
2937: v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
2938: cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
2939: mu1=mu[i][(int) age]/stepm*YEARM ;
2940: mu2=mu[j][(int) age]/stepm*YEARM;
2941: c12=cv12/sqrt(v1*v2);
2942: /* Computing eigen value of matrix of covariance */
2943: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
2944: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
2945: /* Eigen vectors */
2946: v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
2947: /*v21=sqrt(1.-v11*v11); *//* error */
2948: v21=(lc1-v1)/cv12*v11;
2949: v12=-v21;
2950: v22=v11;
2951: tnalp=v21/v11;
2952: if(first1==1){
2953: first1=0;
2954: printf("%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tang %.3f\nOthers in log...\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
2955: }
2956: fprintf(ficlog,"%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tan %.3f\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
2957: /*printf(fignu*/
2958: /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
2959: /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
2960: if(first==1){
2961: first=0;
2962: fprintf(ficgp,"\nset parametric;unset label");
2963: fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
2964: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
2965: fprintf(fichtm,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup> :<a href=\"varpijgr%s%d%1d%1d-%1d%1d.png\">varpijgr%s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,optionfilefiname, j1,k1,l1,k2,l2,optionfilefiname, j1,k1,l1,k2,l2);
2966: fprintf(fichtm,"\n<br><img src=\"varpijgr%s%d%1d%1d-%1d%1d.png\"> ",optionfilefiname, j1,k1,l1,k2,l2);
2967: fprintf(fichtm,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
2968: fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\"",optionfilefiname, j1,k1,l1,k2,l2);
2969: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
2970: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
2971: fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
2972: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
2973: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
2974: }else{
2975: first=0;
2976: fprintf(fichtm," %d (%.3f),",(int) age, c12);
2977: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
2978: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
2979: fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
2980: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
2981: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
2982: }/* if first */
2983: } /* age mod 5 */
2984: } /* end loop age */
2985: fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\";replot;",optionfilefiname, j1,k1,l1,k2,l2);
2986: first=1;
2987: } /*l12 */
2988: } /* k12 */
2989: } /*l1 */
2990: }/* k1 */
2991: } /* loop covariates */
2992: }
1.59 brouard 2993: free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
2994: free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
1.53 brouard 2995: free_vector(xp,1,npar);
2996: fclose(ficresprob);
2997: fclose(ficresprobcov);
2998: fclose(ficresprobcor);
2999: fclose(ficgp);
3000: fclose(fichtm);
3001: }
3002:
3003:
3004: /******************* Printing html file ***********/
3005: void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
3006: int lastpass, int stepm, int weightopt, char model[],\
3007: int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
3008: int popforecast, int estepm ,\
3009: double jprev1, double mprev1,double anprev1, \
3010: double jprev2, double mprev2,double anprev2){
3011: int jj1, k1, i1, cpt;
3012: /*char optionfilehtm[FILENAMELENGTH];*/
3013: if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
3014: printf("Problem with %s \n",optionfilehtm), exit(0);
3015: fprintf(ficlog,"Problem with %s \n",optionfilehtm), exit(0);
3016: }
3017:
1.85 brouard 3018: fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n \
3019: - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"p%s\">p%s</a> <br>\n \
3020: - Estimated transition probabilities over %d (stepm) months: <a href=\"pij%s\">pij%s</a><br>\n \
3021: - Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n \
3022: - Life expectancies by age and initial health status (estepm=%2d months): \
1.53 brouard 3023: <a href=\"e%s\">e%s</a> <br>\n</li>", \
3024: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);
3025:
3026: fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
3027:
3028: m=cptcoveff;
3029: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
3030:
3031: jj1=0;
3032: for(k1=1; k1<=m;k1++){
3033: for(i1=1; i1<=ncodemax[k1];i1++){
3034: jj1++;
3035: if (cptcovn > 0) {
3036: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
3037: for (cpt=1; cpt<=cptcoveff;cpt++)
3038: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
3039: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
3040: }
3041: /* Pij */
1.85 brouard 3042: fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: pe%s%d1.png<br> \
1.53 brouard 3043: <img src=\"pe%s%d1.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
3044: /* Quasi-incidences */
1.85 brouard 3045: fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
3046: before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: pe%s%d2.png<br> \
1.53 brouard 3047: <img src=\"pe%s%d2.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
3048: /* Stable prevalence in each health state */
3049: for(cpt=1; cpt<nlstate;cpt++){
1.85 brouard 3050: fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br> \
1.53 brouard 3051: <img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
3052: }
3053: for(cpt=1; cpt<=nlstate;cpt++) {
1.85 brouard 3054: fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.png <br> \
1.53 brouard 3055: <img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
3056: }
1.85 brouard 3057: fprintf(fichtm,"\n<br>- Total life expectancy by age and \
3058: health expectancies in states (1) and (2): e%s%d.png<br>\
1.53 brouard 3059: <img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
3060: } /* end i1 */
3061: }/* End k1 */
3062: fprintf(fichtm,"</ul>");
3063:
3064:
1.85 brouard 3065: fprintf(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n\
3066: - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n\
3067: - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n\
3068: - Variance-covariance of one-step probabilities: <a href=\"probcov%s\">probcov%s</a> <br>\n\
3069: - Correlation matrix of one-step probabilities: <a href=\"probcor%s\">probcor%s</a> <br>\n\
3070: - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n\
3071: - Health expectancies with their variances (no covariance): <a href=\"t%s\">t%s</a> <br>\n\
1.53 brouard 3072: - Standard deviation of stable prevalences: <a href=\"vpl%s\">vpl%s</a> <br>\n",rfileres,rfileres,fileres,fileres,fileres,fileres,fileres,fileres, estepm, fileres,fileres,fileres,fileres,fileres,fileres);
3073:
1.76 brouard 3074: /* if(popforecast==1) fprintf(fichtm,"\n */
3075: /* - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
3076: /* - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
3077: /* <br>",fileres,fileres,fileres,fileres); */
3078: /* else */
3079: /* fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model); */
1.53 brouard 3080: fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
3081:
3082: m=cptcoveff;
3083: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
3084:
3085: jj1=0;
3086: for(k1=1; k1<=m;k1++){
3087: for(i1=1; i1<=ncodemax[k1];i1++){
3088: jj1++;
3089: if (cptcovn > 0) {
3090: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
3091: for (cpt=1; cpt<=cptcoveff;cpt++)
3092: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
3093: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
3094: }
3095: for(cpt=1; cpt<=nlstate;cpt++) {
1.85 brouard 3096: fprintf(fichtm,"<br>- Observed and period prevalence (with confident\
3097: interval) in state (%d): v%s%d%d.png <br>\
1.53 brouard 3098: <img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
3099: }
3100: } /* end i1 */
3101: }/* End k1 */
3102: fprintf(fichtm,"</ul>");
3103: fclose(fichtm);
3104: }
3105:
3106: /******************* Gnuplot file **************/
3107: void printinggnuplot(char fileres[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
3108:
3109: int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
3110: int ng;
3111: if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
3112: printf("Problem with file %s",optionfilegnuplot);
3113: fprintf(ficlog,"Problem with file %s",optionfilegnuplot);
3114: }
3115:
1.54 brouard 3116: /*#ifdef windows */
1.53 brouard 3117: fprintf(ficgp,"cd \"%s\" \n",pathc);
1.54 brouard 3118: /*#endif */
1.53 brouard 3119: m=pow(2,cptcoveff);
3120:
3121: /* 1eme*/
3122: for (cpt=1; cpt<= nlstate ; cpt ++) {
3123: for (k1=1; k1<= m ; k1 ++) {
3124: fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
3125: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,fileres,k1-1,k1-1);
3126:
3127: for (i=1; i<= nlstate ; i ++) {
3128: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
3129: else fprintf(ficgp," \%%*lf (\%%*lf)");
3130: }
1.69 brouard 3131: fprintf(ficgp,"\" t\"Stable prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+1.96*$3) \"\%%lf",fileres,k1-1,k1-1);
1.53 brouard 3132: for (i=1; i<= nlstate ; i ++) {
3133: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
3134: else fprintf(ficgp," \%%*lf (\%%*lf)");
3135: }
1.69 brouard 3136: fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",fileres,k1-1,k1-1);
1.53 brouard 3137: for (i=1; i<= nlstate ; i ++) {
3138: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
3139: else fprintf(ficgp," \%%*lf (\%%*lf)");
3140: }
3141: fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));
3142: }
3143: }
3144: /*2 eme*/
3145:
3146: for (k1=1; k1<= m ; k1 ++) {
3147: fprintf(ficgp,"\nset out \"e%s%d.png\" \n",strtok(optionfile, "."),k1);
3148: fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
3149:
3150: for (i=1; i<= nlstate+1 ; i ++) {
3151: k=2*i;
3152: fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);
3153: for (j=1; j<= nlstate+1 ; j ++) {
3154: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
3155: else fprintf(ficgp," \%%*lf (\%%*lf)");
3156: }
3157: if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
3158: else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
3159: fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);
3160: for (j=1; j<= nlstate+1 ; j ++) {
3161: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
3162: else fprintf(ficgp," \%%*lf (\%%*lf)");
3163: }
3164: fprintf(ficgp,"\" t\"\" w l 0,");
3165: fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);
3166: for (j=1; j<= nlstate+1 ; j ++) {
3167: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
3168: else fprintf(ficgp," \%%*lf (\%%*lf)");
3169: }
3170: if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
3171: else fprintf(ficgp,"\" t\"\" w l 0,");
3172: }
3173: }
3174:
3175: /*3eme*/
3176:
3177: for (k1=1; k1<= m ; k1 ++) {
3178: for (cpt=1; cpt<= nlstate ; cpt ++) {
3179: k=2+nlstate*(2*cpt-2);
3180: fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
3181: fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);
3182: /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
3183: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
3184: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
3185: fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
3186: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
3187: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
3188:
3189: */
3190: for (i=1; i< nlstate ; i ++) {
3191: fprintf(ficgp," ,\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+2*i,cpt,i+1);
3192:
3193: }
3194: }
3195: }
3196:
1.76 brouard 3197: /* CV preval stable (period) */
1.53 brouard 3198: for (k1=1; k1<= m ; k1 ++) {
1.76 brouard 3199: for (cpt=1; cpt<=nlstate ; cpt ++) {
1.53 brouard 3200: k=3;
3201: fprintf(ficgp,"\nset out \"p%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
3202: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);
3203:
1.83 lievre 3204: for (i=1; i< nlstate ; i ++)
1.53 brouard 3205: fprintf(ficgp,"+$%d",k+i+1);
3206: fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
3207:
3208: l=3+(nlstate+ndeath)*cpt;
3209: fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);
3210: for (i=1; i< nlstate ; i ++) {
3211: l=3+(nlstate+ndeath)*cpt;
3212: fprintf(ficgp,"+$%d",l+i+1);
3213: }
3214: fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);
3215: }
3216: }
3217:
3218: /* proba elementaires */
3219: for(i=1,jk=1; i <=nlstate; i++){
3220: for(k=1; k <=(nlstate+ndeath); k++){
3221: if (k != i) {
3222: for(j=1; j <=ncovmodel; j++){
3223: fprintf(ficgp,"p%d=%f ",jk,p[jk]);
3224: jk++;
3225: fprintf(ficgp,"\n");
3226: }
3227: }
3228: }
3229: }
3230:
3231: for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
3232: for(jk=1; jk <=m; jk++) {
3233: fprintf(ficgp,"\nset out \"pe%s%d%d.png\" \n",strtok(optionfile, "."),jk,ng);
3234: if (ng==2)
3235: fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
3236: else
3237: fprintf(ficgp,"\nset title \"Probability\"\n");
3238: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot [%.f:%.f] ",ageminpar,agemaxpar);
3239: i=1;
3240: for(k2=1; k2<=nlstate; k2++) {
3241: k3=i;
3242: for(k=1; k<=(nlstate+ndeath); k++) {
3243: if (k != k2){
3244: if(ng==2)
3245: fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
3246: else
3247: fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
3248: ij=1;
3249: for(j=3; j <=ncovmodel; j++) {
3250: if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
3251: fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
3252: ij++;
3253: }
3254: else
3255: fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
3256: }
3257: fprintf(ficgp,")/(1");
3258:
3259: for(k1=1; k1 <=nlstate; k1++){
3260: fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
3261: ij=1;
3262: for(j=3; j <=ncovmodel; j++){
3263: if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
3264: fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
3265: ij++;
3266: }
3267: else
3268: fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
3269: }
3270: fprintf(ficgp,")");
3271: }
3272: fprintf(ficgp,") t \"p%d%d\" ", k2,k);
3273: if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
3274: i=i+ncovmodel;
3275: }
3276: } /* end k */
3277: } /* end k2 */
3278: } /* end jk */
3279: } /* end ng */
3280: fclose(ficgp);
3281: } /* end gnuplot */
3282:
3283:
3284: /*************** Moving average **************/
1.54 brouard 3285: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
1.53 brouard 3286:
3287: int i, cpt, cptcod;
1.58 lievre 3288: int modcovmax =1;
1.54 brouard 3289: int mobilavrange, mob;
1.53 brouard 3290: double age;
1.58 lievre 3291:
3292: modcovmax=2*cptcoveff;/* Max number of modalities. We suppose
3293: a covariate has 2 modalities */
3294: if (cptcovn<1) modcovmax=1; /* At least 1 pass */
3295:
1.54 brouard 3296: if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
3297: if(mobilav==1) mobilavrange=5; /* default */
3298: else mobilavrange=mobilav;
3299: for (age=bage; age<=fage; age++)
3300: for (i=1; i<=nlstate;i++)
1.58 lievre 3301: for (cptcod=1;cptcod<=modcovmax;cptcod++)
1.54 brouard 3302: mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
3303: /* We keep the original values on the extreme ages bage, fage and for
3304: fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
3305: we use a 5 terms etc. until the borders are no more concerned.
3306: */
3307: for (mob=3;mob <=mobilavrange;mob=mob+2){
3308: for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
3309: for (i=1; i<=nlstate;i++){
1.58 lievre 3310: for (cptcod=1;cptcod<=modcovmax;cptcod++){
1.54 brouard 3311: mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
3312: for (cpt=1;cpt<=(mob-1)/2;cpt++){
3313: mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
3314: mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
3315: }
3316: mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
3317: }
1.53 brouard 3318: }
1.54 brouard 3319: }/* end age */
3320: }/* end mob */
3321: }else return -1;
3322: return 0;
3323: }/* End movingaverage */
1.53 brouard 3324:
3325:
3326: /************** Forecasting ******************/
1.70 brouard 3327: prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){
1.69 brouard 3328: /* proj1, year, month, day of starting projection
3329: agemin, agemax range of age
3330: dateprev1 dateprev2 range of dates during which prevalence is computed
1.70 brouard 3331: anproj2 year of en of projection (same day and month as proj1).
1.69 brouard 3332: */
1.73 lievre 3333: int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
1.53 brouard 3334: int *popage;
1.70 brouard 3335: double agec; /* generic age */
3336: double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
1.53 brouard 3337: double *popeffectif,*popcount;
3338: double ***p3mat;
1.55 lievre 3339: double ***mobaverage;
1.53 brouard 3340: char fileresf[FILENAMELENGTH];
3341:
1.69 brouard 3342: agelim=AGESUP;
1.84 brouard 3343: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
1.53 brouard 3344:
3345: strcpy(fileresf,"f");
3346: strcat(fileresf,fileres);
3347: if((ficresf=fopen(fileresf,"w"))==NULL) {
3348: printf("Problem with forecast resultfile: %s\n", fileresf);
3349: fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
3350: }
3351: printf("Computing forecasting: result on file '%s' \n", fileresf);
3352: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
3353:
3354: if (cptcoveff==0) ncodemax[cptcoveff]=1;
3355:
1.54 brouard 3356: if (mobilav!=0) {
1.53 brouard 3357: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.54 brouard 3358: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
3359: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
3360: printf(" Error in movingaverage mobilav=%d\n",mobilav);
3361: }
1.53 brouard 3362: }
3363:
3364: stepsize=(int) (stepm+YEARM-1)/YEARM;
3365: if (stepm<=12) stepsize=1;
1.74 brouard 3366: if(estepm < stepm){
3367: printf ("Problem %d lower than %d\n",estepm, stepm);
3368: }
3369: else hstepm=estepm;
3370:
1.53 brouard 3371: hstepm=hstepm/stepm;
1.69 brouard 3372: yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp and
3373: fractional in yp1 */
1.53 brouard 3374: anprojmean=yp;
3375: yp2=modf((yp1*12),&yp);
3376: mprojmean=yp;
3377: yp1=modf((yp2*30.5),&yp);
3378: jprojmean=yp;
3379: if(jprojmean==0) jprojmean=1;
3380: if(mprojmean==0) jprojmean=1;
1.73 lievre 3381:
3382: i1=cptcoveff;
3383: if (cptcovn < 1){i1=1;}
1.53 brouard 3384:
1.70 brouard 3385: fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
1.53 brouard 3386:
1.70 brouard 3387: fprintf(ficresf,"#****** Routine prevforecast **\n");
1.73 lievre 3388:
1.75 brouard 3389: /* if (h==(int)(YEARM*yearp)){ */
1.73 lievre 3390: for(cptcov=1, k=0;cptcov<=i1;cptcov++){
1.53 brouard 3391: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
3392: k=k+1;
3393: fprintf(ficresf,"\n#******");
3394: for(j=1;j<=cptcoveff;j++) {
1.70 brouard 3395: fprintf(ficresf," V%d=%d, hpijx=probability over h years, hp.jx is weighted by observed prev ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
1.53 brouard 3396: }
3397: fprintf(ficresf,"******\n");
1.70 brouard 3398: fprintf(ficresf,"# Covariate valuofcovar yearproj age");
3399: for(j=1; j<=nlstate+ndeath;j++){
3400: for(i=1; i<=nlstate;i++)
3401: fprintf(ficresf," p%d%d",i,j);
3402: fprintf(ficresf," p.%d",j);
3403: }
1.74 brouard 3404: for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
1.53 brouard 3405: fprintf(ficresf,"\n");
1.70 brouard 3406: fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
1.53 brouard 3407:
1.71 brouard 3408: for (agec=fage; agec>=(ageminpar-1); agec--){
1.70 brouard 3409: nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
1.53 brouard 3410: nhstepm = nhstepm/hstepm;
3411: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3412: oldm=oldms;savm=savms;
1.70 brouard 3413: hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
1.53 brouard 3414:
3415: for (h=0; h<=nhstepm; h++){
1.75 brouard 3416: if (h*hstepm/YEARM*stepm ==yearp) {
1.69 brouard 3417: fprintf(ficresf,"\n");
3418: for(j=1;j<=cptcoveff;j++)
3419: fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
1.70 brouard 3420: fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
1.53 brouard 3421: }
3422: for(j=1; j<=nlstate+ndeath;j++) {
1.70 brouard 3423: ppij=0.;
1.71 brouard 3424: for(i=1; i<=nlstate;i++) {
1.53 brouard 3425: if (mobilav==1)
1.71 brouard 3426: ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
1.53 brouard 3427: else {
1.71 brouard 3428: ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
1.53 brouard 3429: }
1.75 brouard 3430: if (h*hstepm/YEARM*stepm== yearp) {
1.70 brouard 3431: fprintf(ficresf," %.3f", p3mat[i][j][h]);
1.75 brouard 3432: }
3433: } /* end i */
3434: if (h*hstepm/YEARM*stepm==yearp) {
1.70 brouard 3435: fprintf(ficresf," %.3f", ppij);
1.53 brouard 3436: }
1.75 brouard 3437: }/* end j */
3438: } /* end h */
1.53 brouard 3439: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
1.75 brouard 3440: } /* end agec */
3441: } /* end yearp */
3442: } /* end cptcod */
3443: } /* end cptcov */
1.53 brouard 3444:
1.54 brouard 3445: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.53 brouard 3446:
3447: fclose(ficresf);
3448: }
1.70 brouard 3449:
3450: /************** Forecasting *****not tested NB*************/
1.53 brouard 3451: populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){
3452:
3453: int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
3454: int *popage;
1.69 brouard 3455: double calagedatem, agelim, kk1, kk2;
1.53 brouard 3456: double *popeffectif,*popcount;
3457: double ***p3mat,***tabpop,***tabpopprev;
1.55 lievre 3458: double ***mobaverage;
1.53 brouard 3459: char filerespop[FILENAMELENGTH];
3460:
3461: tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3462: tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3463: agelim=AGESUP;
1.69 brouard 3464: calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
1.53 brouard 3465:
1.84 brouard 3466: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
1.53 brouard 3467:
3468:
3469: strcpy(filerespop,"pop");
3470: strcat(filerespop,fileres);
3471: if((ficrespop=fopen(filerespop,"w"))==NULL) {
3472: printf("Problem with forecast resultfile: %s\n", filerespop);
3473: fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
3474: }
3475: printf("Computing forecasting: result on file '%s' \n", filerespop);
3476: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
3477:
3478: if (cptcoveff==0) ncodemax[cptcoveff]=1;
3479:
1.54 brouard 3480: if (mobilav!=0) {
1.53 brouard 3481: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.54 brouard 3482: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
3483: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
3484: printf(" Error in movingaverage mobilav=%d\n",mobilav);
3485: }
1.53 brouard 3486: }
3487:
3488: stepsize=(int) (stepm+YEARM-1)/YEARM;
3489: if (stepm<=12) stepsize=1;
3490:
3491: agelim=AGESUP;
3492:
3493: hstepm=1;
3494: hstepm=hstepm/stepm;
3495:
3496: if (popforecast==1) {
3497: if((ficpop=fopen(popfile,"r"))==NULL) {
3498: printf("Problem with population file : %s\n",popfile);exit(0);
3499: fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
3500: }
3501: popage=ivector(0,AGESUP);
3502: popeffectif=vector(0,AGESUP);
3503: popcount=vector(0,AGESUP);
3504:
3505: i=1;
3506: while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
3507:
3508: imx=i;
3509: for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
3510: }
3511:
1.69 brouard 3512: for(cptcov=1,k=0;cptcov<=i2;cptcov++){
1.53 brouard 3513: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
3514: k=k+1;
3515: fprintf(ficrespop,"\n#******");
3516: for(j=1;j<=cptcoveff;j++) {
3517: fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
3518: }
3519: fprintf(ficrespop,"******\n");
3520: fprintf(ficrespop,"# Age");
3521: for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
3522: if (popforecast==1) fprintf(ficrespop," [Population]");
3523:
3524: for (cpt=0; cpt<=0;cpt++) {
3525: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
3526:
1.69 brouard 3527: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
1.53 brouard 3528: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
3529: nhstepm = nhstepm/hstepm;
3530:
3531: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3532: oldm=oldms;savm=savms;
3533: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
3534:
3535: for (h=0; h<=nhstepm; h++){
1.69 brouard 3536: if (h==(int) (calagedatem+YEARM*cpt)) {
1.53 brouard 3537: fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
3538: }
3539: for(j=1; j<=nlstate+ndeath;j++) {
3540: kk1=0.;kk2=0;
3541: for(i=1; i<=nlstate;i++) {
3542: if (mobilav==1)
3543: kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
3544: else {
3545: kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
3546: }
3547: }
1.69 brouard 3548: if (h==(int)(calagedatem+12*cpt)){
1.53 brouard 3549: tabpop[(int)(agedeb)][j][cptcod]=kk1;
3550: /*fprintf(ficrespop," %.3f", kk1);
3551: if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
3552: }
3553: }
3554: for(i=1; i<=nlstate;i++){
3555: kk1=0.;
3556: for(j=1; j<=nlstate;j++){
3557: kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
3558: }
1.69 brouard 3559: tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
1.53 brouard 3560: }
3561:
1.69 brouard 3562: if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++)
1.53 brouard 3563: fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
3564: }
3565: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3566: }
3567: }
3568:
3569: /******/
3570:
3571: for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
3572: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
1.69 brouard 3573: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
1.53 brouard 3574: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
3575: nhstepm = nhstepm/hstepm;
3576:
3577: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3578: oldm=oldms;savm=savms;
3579: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
3580: for (h=0; h<=nhstepm; h++){
1.69 brouard 3581: if (h==(int) (calagedatem+YEARM*cpt)) {
1.53 brouard 3582: fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
3583: }
3584: for(j=1; j<=nlstate+ndeath;j++) {
3585: kk1=0.;kk2=0;
3586: for(i=1; i<=nlstate;i++) {
3587: kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
3588: }
1.69 brouard 3589: if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);
1.53 brouard 3590: }
3591: }
3592: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3593: }
3594: }
3595: }
3596: }
3597:
1.54 brouard 3598: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.53 brouard 3599:
3600: if (popforecast==1) {
3601: free_ivector(popage,0,AGESUP);
3602: free_vector(popeffectif,0,AGESUP);
3603: free_vector(popcount,0,AGESUP);
3604: }
3605: free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3606: free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3607: fclose(ficrespop);
1.84 brouard 3608: } /* End of popforecast */
1.53 brouard 3609:
1.86 ! brouard 3610: int fileappend(FILE *fichier, char *optionfile)
! 3611: {
! 3612: if((fichier=fopen(optionfile,"a"))==NULL) {
! 3613: printf("Problem with file: %s\n", optionfile);
! 3614: fprintf(ficlog,"Problem with file: %s\n", optionfile);
! 3615: return (1);
! 3616: }
! 3617:
! 3618: }
1.53 brouard 3619: /***********************************************/
3620: /**************** Main Program *****************/
3621: /***********************************************/
3622:
3623: int main(int argc, char *argv[])
3624: {
1.61 brouard 3625: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
1.74 brouard 3626: int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
1.85 brouard 3627: int jj;
3628: int numlinepar=0; /* Current linenumber of parameter file */
1.53 brouard 3629: double agedeb, agefin,hf;
3630: double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
3631:
3632: double fret;
3633: double **xi,tmp,delta;
3634:
3635: double dum; /* Dummy variable */
3636: double ***p3mat;
3637: double ***mobaverage;
3638: int *indx;
3639: char line[MAXLINE], linepar[MAXLINE];
1.85 brouard 3640: char path[132],pathc[132],pathcd[132],pathtot[132],model[132];
1.53 brouard 3641: int firstobs=1, lastobs=10;
3642: int sdeb, sfin; /* Status at beginning and end */
3643: int c, h , cpt,l;
3644: int ju,jl, mi;
3645: int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
1.59 brouard 3646: int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab;
1.69 brouard 3647: int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
1.53 brouard 3648: int mobilav=0,popforecast=0;
3649: int hstepm, nhstepm;
1.74 brouard 3650: double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
3651: double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
1.53 brouard 3652:
3653: double bage, fage, age, agelim, agebase;
3654: double ftolpl=FTOL;
3655: double **prlim;
3656: double *severity;
3657: double ***param; /* Matrix of parameters */
3658: double *p;
3659: double **matcov; /* Matrix of covariance */
3660: double ***delti3; /* Scale */
3661: double *delti; /* Scale */
3662: double ***eij, ***vareij;
3663: double **varpl; /* Variances of prevalence limits by age */
3664: double *epj, vepp;
3665: double kk1, kk2;
1.74 brouard 3666: double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
1.53 brouard 3667:
3668: char *alph[]={"a","a","b","c","d","e"}, str[4];
3669:
3670:
3671: char z[1]="c", occ;
1.86 ! brouard 3672:
1.53 brouard 3673: char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
1.85 brouard 3674: char *strt, *strtend;
3675: char *stratrunc;
3676: int lstra;
3677:
3678: long total_usecs;
3679: struct timeval start_time, end_time, curr_time;
3680: struct timezone tzp;
3681: extern int gettimeofday();
3682: struct tm tmg, tm, *gmtime(), *localtime();
3683: long time_value;
3684: extern long time();
1.53 brouard 3685:
1.85 brouard 3686: /* gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
3687: (void) gettimeofday(&start_time,&tzp);
3688: tm = *localtime(&start_time.tv_sec);
3689: tmg = *gmtime(&start_time.tv_sec);
3690: strt=asctime(&tm);
1.86 ! brouard 3691:
1.85 brouard 3692: /* printf("Localtime (at start)=%s",strt); */
3693: /* tp.tv_sec = tp.tv_sec +86400; */
3694: /* tm = *localtime(&start_time.tv_sec); */
3695: /* tmg.tm_year=tmg.tm_year +dsign*dyear; */
3696: /* tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
3697: /* tmg.tm_hour=tmg.tm_hour + 1; */
3698: /* tp.tv_sec = mktime(&tmg); */
3699: /* strt=asctime(&tmg); */
3700: /* printf("Time(after) =%s",strt); */
3701: /* (void) time (&time_value);
3702: * printf("time=%d,t-=%d\n",time_value,time_value-86400);
3703: * tm = *localtime(&time_value);
3704: * strt=asctime(&tm);
3705: * printf("tim_value=%d,asctime=%s\n",time_value,strt);
3706: */
3707:
1.53 brouard 3708: getcwd(pathcd, size);
3709:
1.81 brouard 3710: printf("\n%s\n%s",version,fullversion);
1.53 brouard 3711: if(argc <=1){
3712: printf("\nEnter the parameter file name: ");
3713: scanf("%s",pathtot);
3714: }
3715: else{
3716: strcpy(pathtot,argv[1]);
3717: }
1.85 brouard 3718: /*if(getcwd(pathcd, 132)!= NULL)printf ("Error pathcd\n");*/
1.53 brouard 3719: /*cygwin_split_path(pathtot,path,optionfile);
3720: printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
3721: /* cutv(path,optionfile,pathtot,'\\');*/
3722:
3723: split(pathtot,path,optionfile,optionfilext,optionfilefiname);
1.85 brouard 3724: printf("pathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
1.53 brouard 3725: chdir(path);
3726: replace(pathc,path);
3727:
1.59 brouard 3728: /*-------- arguments in the command line --------*/
1.53 brouard 3729:
3730: /* Log file */
3731: strcat(filelog, optionfilefiname);
3732: strcat(filelog,".log"); /* */
3733: if((ficlog=fopen(filelog,"w"))==NULL) {
3734: printf("Problem with logfile %s\n",filelog);
3735: goto end;
3736: }
3737: fprintf(ficlog,"Log filename:%s\n",filelog);
1.85 brouard 3738: fprintf(ficlog,"\n%s\n%s",version,fullversion);
1.53 brouard 3739: fprintf(ficlog,"\nEnter the parameter file name: ");
3740: fprintf(ficlog,"pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
1.86 ! brouard 3741:
! 3742: printf("Localtime (at start)=%s",strt);
! 3743: fprintf(ficlog,"Localtime (at start)=%s",strt);
1.53 brouard 3744: fflush(ficlog);
3745:
3746: /* */
3747: strcpy(fileres,"r");
3748: strcat(fileres, optionfilefiname);
3749: strcat(fileres,".txt"); /* Other files have txt extension */
3750:
3751: /*---------arguments file --------*/
3752:
3753: if((ficpar=fopen(optionfile,"r"))==NULL) {
3754: printf("Problem with optionfile %s\n",optionfile);
3755: fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
1.85 brouard 3756: fflush(ficlog);
1.53 brouard 3757: goto end;
3758: }
3759:
3760: strcpy(filereso,"o");
3761: strcat(filereso,fileres);
3762: if((ficparo=fopen(filereso,"w"))==NULL) {
3763: printf("Problem with Output resultfile: %s\n", filereso);
3764: fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
1.85 brouard 3765: fflush(ficlog);
1.53 brouard 3766: goto end;
3767: }
3768:
3769: /* Reads comments: lines beginning with '#' */
1.85 brouard 3770: numlinepar=0;
1.53 brouard 3771: while((c=getc(ficpar))=='#' && c!= EOF){
3772: ungetc(c,ficpar);
3773: fgets(line, MAXLINE, ficpar);
1.85 brouard 3774: numlinepar++;
1.53 brouard 3775: puts(line);
3776: fputs(line,ficparo);
1.85 brouard 3777: fputs(line,ficlog);
1.53 brouard 3778: }
3779: ungetc(c,ficpar);
3780:
3781: fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
1.85 brouard 3782: numlinepar++;
1.53 brouard 3783: printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);
3784: fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
1.85 brouard 3785: fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
3786: fflush(ficlog);
1.59 brouard 3787: while((c=getc(ficpar))=='#' && c!= EOF){
1.53 brouard 3788: ungetc(c,ficpar);
3789: fgets(line, MAXLINE, ficpar);
1.85 brouard 3790: numlinepar++;
1.53 brouard 3791: puts(line);
3792: fputs(line,ficparo);
1.85 brouard 3793: fputs(line,ficlog);
1.53 brouard 3794: }
3795: ungetc(c,ficpar);
1.85 brouard 3796:
1.53 brouard 3797:
3798: covar=matrix(0,NCOVMAX,1,n);
1.58 lievre 3799: cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
1.53 brouard 3800: if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
3801:
1.58 lievre 3802: ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
1.53 brouard 3803: nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
3804:
3805: /* Read guess parameters */
3806: /* Reads comments: lines beginning with '#' */
3807: while((c=getc(ficpar))=='#' && c!= EOF){
3808: ungetc(c,ficpar);
3809: fgets(line, MAXLINE, ficpar);
1.85 brouard 3810: numlinepar++;
1.53 brouard 3811: puts(line);
3812: fputs(line,ficparo);
1.85 brouard 3813: fputs(line,ficlog);
1.53 brouard 3814: }
3815: ungetc(c,ficpar);
1.85 brouard 3816:
1.53 brouard 3817: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
1.85 brouard 3818: for(i=1; i <=nlstate; i++){
3819: j=0;
3820: for(jj=1; jj <=nlstate+ndeath; jj++){
3821: if(jj==i) continue;
3822: j++;
1.53 brouard 3823: fscanf(ficpar,"%1d%1d",&i1,&j1);
1.85 brouard 3824: if ((i1 != i) && (j1 != j)){
3825: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
3826: exit(1);
3827: }
1.53 brouard 3828: fprintf(ficparo,"%1d%1d",i1,j1);
3829: if(mle==1)
3830: printf("%1d%1d",i,j);
3831: fprintf(ficlog,"%1d%1d",i,j);
3832: for(k=1; k<=ncovmodel;k++){
3833: fscanf(ficpar," %lf",¶m[i][j][k]);
3834: if(mle==1){
3835: printf(" %lf",param[i][j][k]);
3836: fprintf(ficlog," %lf",param[i][j][k]);
3837: }
3838: else
3839: fprintf(ficlog," %lf",param[i][j][k]);
3840: fprintf(ficparo," %lf",param[i][j][k]);
3841: }
3842: fscanf(ficpar,"\n");
1.85 brouard 3843: numlinepar++;
1.53 brouard 3844: if(mle==1)
3845: printf("\n");
3846: fprintf(ficlog,"\n");
3847: fprintf(ficparo,"\n");
3848: }
1.85 brouard 3849: }
3850: fflush(ficlog);
3851:
1.59 brouard 3852: npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
1.53 brouard 3853:
3854: p=param[1][1];
3855:
3856: /* Reads comments: lines beginning with '#' */
3857: while((c=getc(ficpar))=='#' && c!= EOF){
3858: ungetc(c,ficpar);
3859: fgets(line, MAXLINE, ficpar);
1.85 brouard 3860: numlinepar++;
1.53 brouard 3861: puts(line);
3862: fputs(line,ficparo);
1.85 brouard 3863: fputs(line,ficlog);
1.53 brouard 3864: }
3865: ungetc(c,ficpar);
3866:
3867: delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
1.74 brouard 3868: /* delti=vector(1,npar); *//* Scale of each paramater (output from hesscov) */
1.53 brouard 3869: for(i=1; i <=nlstate; i++){
3870: for(j=1; j <=nlstate+ndeath-1; j++){
3871: fscanf(ficpar,"%1d%1d",&i1,&j1);
1.85 brouard 3872: if ((i1-i)*(j1-j)!=0){
3873: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
3874: exit(1);
3875: }
1.53 brouard 3876: printf("%1d%1d",i,j);
3877: fprintf(ficparo,"%1d%1d",i1,j1);
1.85 brouard 3878: fprintf(ficlog,"%1d%1d",i1,j1);
1.53 brouard 3879: for(k=1; k<=ncovmodel;k++){
3880: fscanf(ficpar,"%le",&delti3[i][j][k]);
3881: printf(" %le",delti3[i][j][k]);
3882: fprintf(ficparo," %le",delti3[i][j][k]);
1.85 brouard 3883: fprintf(ficlog," %le",delti3[i][j][k]);
1.53 brouard 3884: }
3885: fscanf(ficpar,"\n");
1.85 brouard 3886: numlinepar++;
1.53 brouard 3887: printf("\n");
3888: fprintf(ficparo,"\n");
1.85 brouard 3889: fprintf(ficlog,"\n");
1.53 brouard 3890: }
3891: }
1.85 brouard 3892: fflush(ficlog);
3893:
1.53 brouard 3894: delti=delti3[1][1];
1.74 brouard 3895:
3896:
3897: /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
1.53 brouard 3898:
3899: /* Reads comments: lines beginning with '#' */
3900: while((c=getc(ficpar))=='#' && c!= EOF){
3901: ungetc(c,ficpar);
3902: fgets(line, MAXLINE, ficpar);
1.85 brouard 3903: numlinepar++;
1.53 brouard 3904: puts(line);
3905: fputs(line,ficparo);
1.85 brouard 3906: fputs(line,ficlog);
1.53 brouard 3907: }
3908: ungetc(c,ficpar);
3909:
3910: matcov=matrix(1,npar,1,npar);
3911: for(i=1; i <=npar; i++){
3912: fscanf(ficpar,"%s",&str);
3913: if(mle==1)
3914: printf("%s",str);
3915: fprintf(ficlog,"%s",str);
3916: fprintf(ficparo,"%s",str);
3917: for(j=1; j <=i; j++){
3918: fscanf(ficpar," %le",&matcov[i][j]);
3919: if(mle==1){
3920: printf(" %.5le",matcov[i][j]);
3921: }
1.85 brouard 3922: fprintf(ficlog," %.5le",matcov[i][j]);
1.53 brouard 3923: fprintf(ficparo," %.5le",matcov[i][j]);
3924: }
3925: fscanf(ficpar,"\n");
1.85 brouard 3926: numlinepar++;
1.53 brouard 3927: if(mle==1)
3928: printf("\n");
3929: fprintf(ficlog,"\n");
3930: fprintf(ficparo,"\n");
3931: }
3932: for(i=1; i <=npar; i++)
3933: for(j=i+1;j<=npar;j++)
3934: matcov[i][j]=matcov[j][i];
3935:
3936: if(mle==1)
3937: printf("\n");
3938: fprintf(ficlog,"\n");
3939:
1.85 brouard 3940: fflush(ficlog);
1.53 brouard 3941:
1.59 brouard 3942: /*-------- Rewriting paramater file ----------*/
3943: strcpy(rfileres,"r"); /* "Rparameterfile */
3944: strcat(rfileres,optionfilefiname); /* Parameter file first name*/
3945: strcat(rfileres,"."); /* */
3946: strcat(rfileres,optionfilext); /* Other files have txt extension */
3947: if((ficres =fopen(rfileres,"w"))==NULL) {
3948: printf("Problem writing new parameter file: %s\n", fileres);goto end;
3949: fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
3950: }
3951: fprintf(ficres,"#%s\n",version);
1.53 brouard 3952:
1.59 brouard 3953: /*-------- data file ----------*/
3954: if((fic=fopen(datafile,"r"))==NULL) {
3955: printf("Problem with datafile: %s\n", datafile);goto end;
3956: fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end;
3957: }
3958:
3959: n= lastobs;
3960: severity = vector(1,maxwav);
3961: outcome=imatrix(1,maxwav+1,1,n);
1.85 brouard 3962: num=lvector(1,n);
1.59 brouard 3963: moisnais=vector(1,n);
3964: annais=vector(1,n);
3965: moisdc=vector(1,n);
3966: andc=vector(1,n);
3967: agedc=vector(1,n);
3968: cod=ivector(1,n);
3969: weight=vector(1,n);
3970: for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
3971: mint=matrix(1,maxwav,1,n);
3972: anint=matrix(1,maxwav,1,n);
3973: s=imatrix(1,maxwav+1,1,n);
3974: tab=ivector(1,NCOVMAX);
3975: ncodemax=ivector(1,8);
3976:
3977: i=1;
3978: while (fgets(line, MAXLINE, fic) != NULL) {
3979: if ((i >= firstobs) && (i <=lastobs)) {
1.53 brouard 3980:
1.59 brouard 3981: for (j=maxwav;j>=1;j--){
3982: cutv(stra, strb,line,' '); s[j][i]=atoi(strb);
3983: strcpy(line,stra);
3984: cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
3985: cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
3986: }
1.53 brouard 3987:
1.59 brouard 3988: cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);
3989: cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);
1.53 brouard 3990:
1.59 brouard 3991: cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);
3992: cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);
1.53 brouard 3993:
1.59 brouard 3994: cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);
3995: for (j=ncovcol;j>=1;j--){
3996: cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);
3997: }
1.85 brouard 3998: lstra=strlen(stra);
3999: if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
4000: stratrunc = &(stra[lstra-9]);
4001: num[i]=atol(stratrunc);
4002: }
4003: else
4004: num[i]=atol(stra);
1.53 brouard 4005:
1.59 brouard 4006: /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
1.85 brouard 4007: printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]), (mint[2][i]), (anint[2][i]), (s[2][i]), (mint[3][i]), (anint[3][i]), (s[3][i]), (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/
1.53 brouard 4008:
1.59 brouard 4009: i=i+1;
4010: }
4011: }
4012: /* printf("ii=%d", ij);
4013: scanf("%d",i);*/
1.53 brouard 4014: imx=i-1; /* Number of individuals */
4015:
4016: /* for (i=1; i<=imx; i++){
4017: if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
4018: if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
4019: if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
4020: }*/
4021: /* for (i=1; i<=imx; i++){
4022: if (s[4][i]==9) s[4][i]=-1;
1.85 brouard 4023: printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]), (mint[2][i]), (anint[2][i]), (s[2][i]), (mint[3][i]), (anint[3][i]), (s[3][i]), (mint[4][i]), (anint[4][i]), (s[4][i]));}*/
1.53 brouard 4024:
1.71 brouard 4025: for (i=1; i<=imx; i++)
1.53 brouard 4026:
1.71 brouard 4027: /*if ((s[3][i]==3) || (s[4][i]==3)) weight[i]=0.08;
4028: else weight[i]=1;*/
4029:
1.53 brouard 4030: /* Calculation of the number of parameter from char model*/
4031: Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
4032: Tprod=ivector(1,15);
4033: Tvaraff=ivector(1,15);
4034: Tvard=imatrix(1,15,1,2);
4035: Tage=ivector(1,15);
4036:
1.58 lievre 4037: if (strlen(model) >1){ /* If there is at least 1 covariate */
1.53 brouard 4038: j=0, j1=0, k1=1, k2=1;
1.58 lievre 4039: j=nbocc(model,'+'); /* j=Number of '+' */
4040: j1=nbocc(model,'*'); /* j1=Number of '*' */
4041: cptcovn=j+1;
4042: cptcovprod=j1; /*Number of products */
1.53 brouard 4043:
4044: strcpy(modelsav,model);
4045: if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
4046: printf("Error. Non available option model=%s ",model);
4047: fprintf(ficlog,"Error. Non available option model=%s ",model);
4048: goto end;
4049: }
4050:
1.59 brouard 4051: /* This loop fills the array Tvar from the string 'model'.*/
1.58 lievre 4052:
1.53 brouard 4053: for(i=(j+1); i>=1;i--){
4054: cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */
1.59 brouard 4055: if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
1.53 brouard 4056: /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
4057: /*scanf("%d",i);*/
4058: if (strchr(strb,'*')) { /* Model includes a product */
4059: cutv(strd,strc,strb,'*'); /* strd*strc Vm*Vn (if not *age)*/
4060: if (strcmp(strc,"age")==0) { /* Vn*age */
4061: cptcovprod--;
4062: cutv(strb,stre,strd,'V');
4063: Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/
4064: cptcovage++;
4065: Tage[cptcovage]=i;
4066: /*printf("stre=%s ", stre);*/
4067: }
4068: else if (strcmp(strd,"age")==0) { /* or age*Vn */
4069: cptcovprod--;
4070: cutv(strb,stre,strc,'V');
4071: Tvar[i]=atoi(stre);
4072: cptcovage++;
4073: Tage[cptcovage]=i;
4074: }
4075: else { /* Age is not in the model */
4076: cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/
4077: Tvar[i]=ncovcol+k1;
4078: cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
4079: Tprod[k1]=i;
4080: Tvard[k1][1]=atoi(strc); /* m*/
4081: Tvard[k1][2]=atoi(stre); /* n */
4082: Tvar[cptcovn+k2]=Tvard[k1][1];
4083: Tvar[cptcovn+k2+1]=Tvard[k1][2];
4084: for (k=1; k<=lastobs;k++)
4085: covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
4086: k1++;
4087: k2=k2+2;
4088: }
4089: }
4090: else { /* no more sum */
4091: /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
4092: /* scanf("%d",i);*/
4093: cutv(strd,strc,strb,'V');
4094: Tvar[i]=atoi(strc);
4095: }
4096: strcpy(modelsav,stra);
4097: /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
4098: scanf("%d",i);*/
4099: } /* end of loop + */
4100: } /* end model */
4101:
1.58 lievre 4102: /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
4103: If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
4104:
1.53 brouard 4105: /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
4106: printf("cptcovprod=%d ", cptcovprod);
4107: fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
1.58 lievre 4108:
4109: scanf("%d ",i);
4110: fclose(fic);*/
1.53 brouard 4111:
4112: /* if(mle==1){*/
1.59 brouard 4113: if (weightopt != 1) { /* Maximisation without weights*/
4114: for(i=1;i<=n;i++) weight[i]=1.0;
4115: }
1.53 brouard 4116: /*-calculation of age at interview from date of interview and age at death -*/
1.59 brouard 4117: agev=matrix(1,maxwav,1,imx);
1.53 brouard 4118:
1.59 brouard 4119: for (i=1; i<=imx; i++) {
4120: for(m=2; (m<= maxwav); m++) {
1.76 brouard 4121: if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
1.59 brouard 4122: anint[m][i]=9999;
4123: s[m][i]=-1;
4124: }
1.76 brouard 4125: if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
1.85 brouard 4126: printf("Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
4127: fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
1.76 brouard 4128: s[m][i]=-1;
4129: }
4130: if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
1.85 brouard 4131: printf("Error! Month of death of individual %ld on line %d was unknown %2d, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,(int)moisdc[i]);
4132: fprintf(ficlog,"Error! Month of death of individual %ld on line %d was unknown %f, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,moisdc[i]);
1.84 brouard 4133: s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
1.76 brouard 4134: }
1.53 brouard 4135: }
1.59 brouard 4136: }
1.53 brouard 4137:
1.59 brouard 4138: for (i=1; i<=imx; i++) {
4139: agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
1.71 brouard 4140: for(m=firstpass; (m<= lastpass); m++){
1.69 brouard 4141: if(s[m][i] >0){
1.59 brouard 4142: if (s[m][i] >= nlstate+1) {
4143: if(agedc[i]>0)
1.76 brouard 4144: if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
1.69 brouard 4145: agev[m][i]=agedc[i];
1.59 brouard 4146: /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
4147: else {
1.76 brouard 4148: if ((int)andc[i]!=9999){
1.85 brouard 4149: printf("Warning negative age at death: %ld line:%d\n",num[i],i);
4150: fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
1.59 brouard 4151: agev[m][i]=-1;
1.53 brouard 4152: }
4153: }
1.70 brouard 4154: }
1.69 brouard 4155: else if(s[m][i] !=9){ /* Standard case, age in fractional
4156: years but with the precision of a
4157: month */
1.59 brouard 4158: agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
1.76 brouard 4159: if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
1.59 brouard 4160: agev[m][i]=1;
4161: else if(agev[m][i] <agemin){
4162: agemin=agev[m][i];
4163: /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
1.53 brouard 4164: }
1.59 brouard 4165: else if(agev[m][i] >agemax){
4166: agemax=agev[m][i];
4167: /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
1.53 brouard 4168: }
1.59 brouard 4169: /*agev[m][i]=anint[m][i]-annais[i];*/
4170: /* agev[m][i] = age[i]+2*m;*/
1.53 brouard 4171: }
1.59 brouard 4172: else { /* =9 */
1.53 brouard 4173: agev[m][i]=1;
1.59 brouard 4174: s[m][i]=-1;
4175: }
1.53 brouard 4176: }
1.59 brouard 4177: else /*= 0 Unknown */
4178: agev[m][i]=1;
4179: }
1.53 brouard 4180:
1.59 brouard 4181: }
4182: for (i=1; i<=imx; i++) {
1.71 brouard 4183: for(m=firstpass; (m<=lastpass); m++){
1.59 brouard 4184: if (s[m][i] > (nlstate+ndeath)) {
4185: printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);
4186: fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);
4187: goto end;
1.53 brouard 4188: }
4189: }
1.59 brouard 4190: }
1.53 brouard 4191:
1.71 brouard 4192: /*for (i=1; i<=imx; i++){
4193: for (m=firstpass; (m<lastpass); m++){
1.85 brouard 4194: printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
1.71 brouard 4195: }
4196:
4197: }*/
4198:
1.59 brouard 4199: printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
4200: fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
4201:
4202: free_vector(severity,1,maxwav);
4203: free_imatrix(outcome,1,maxwav+1,1,n);
4204: free_vector(moisnais,1,n);
4205: free_vector(annais,1,n);
4206: /* free_matrix(mint,1,maxwav,1,n);
4207: free_matrix(anint,1,maxwav,1,n);*/
4208: free_vector(moisdc,1,n);
4209: free_vector(andc,1,n);
1.53 brouard 4210:
4211:
1.59 brouard 4212: wav=ivector(1,imx);
4213: dh=imatrix(1,lastpass-firstpass+1,1,imx);
4214: bh=imatrix(1,lastpass-firstpass+1,1,imx);
4215: mw=imatrix(1,lastpass-firstpass+1,1,imx);
1.69 brouard 4216:
1.59 brouard 4217: /* Concatenates waves */
4218: concatwav(wav, dh, bh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm);
1.53 brouard 4219:
1.59 brouard 4220: /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
1.53 brouard 4221:
1.59 brouard 4222: Tcode=ivector(1,100);
4223: nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
4224: ncodemax[1]=1;
4225: if (cptcovn > 0) tricode(Tvar,nbcode,imx);
1.53 brouard 4226:
1.59 brouard 4227: codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of
4228: the estimations*/
4229: h=0;
4230: m=pow(2,cptcoveff);
1.53 brouard 4231:
1.59 brouard 4232: for(k=1;k<=cptcoveff; k++){
4233: for(i=1; i <=(m/pow(2,k));i++){
4234: for(j=1; j <= ncodemax[k]; j++){
4235: for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
4236: h++;
4237: if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
4238: /* printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/
4239: }
4240: }
4241: }
4242: }
4243: /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
4244: codtab[1][2]=1;codtab[2][2]=2; */
4245: /* for(i=1; i <=m ;i++){
4246: for(k=1; k <=cptcovn; k++){
4247: printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
4248: }
4249: printf("\n");
1.53 brouard 4250: }
1.59 brouard 4251: scanf("%d",i);*/
1.53 brouard 4252:
1.86 ! brouard 4253: /*------------ gnuplot -------------*/
! 4254: strcpy(optionfilegnuplot,optionfilefiname);
! 4255: strcat(optionfilegnuplot,".gp");
! 4256: if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
! 4257: printf("Problem with file %s",optionfilegnuplot);
! 4258: }
! 4259: else{
! 4260: fprintf(ficgp,"\n# %s\n", version);
! 4261: fprintf(ficgp,"# %s\n", optionfilegnuplot);
! 4262: fprintf(ficgp,"set missing 'NaNq'\n");
! 4263: }
! 4264: fclose(ficgp);
! 4265: /*--------- index.htm --------*/
! 4266:
! 4267: strcpy(optionfilehtm,optionfile);
! 4268: strcat(optionfilehtm,".htm");
! 4269: if((fichtm=fopen(optionfilehtm,"w"))==NULL) {
! 4270: printf("Problem with %s \n",optionfilehtm), exit(0);
! 4271: }
! 4272:
! 4273: fprintf(fichtm,"<body> <font size=\"2\">%s <br> %s</font> \
! 4274: <hr size=\"2\" color=\"#EC5E5E\"> \n\
! 4275: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
! 4276: \n\
! 4277: <hr size=\"2\" color=\"#EC5E5E\">\
! 4278: <ul><li><h4>Parameter files</h4>\n\
! 4279: - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
! 4280: - Log file of the run: <a href=\"%s\">%s</a><br>\n\
! 4281: - Gnuplot file name: <a href=\"%s\">%s</a>\n\
! 4282: - Date and time at start: %s</ul>\n",\
! 4283: version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt,\
! 4284: model,fileres,fileres,\
! 4285: filelog,filelog,optionfilegnuplot,optionfilegnuplot,strt);
! 4286: fclose(fichtm);
! 4287:
1.59 brouard 4288: /* Calculates basic frequencies. Computes observed prevalence at single age
4289: and prints on file fileres'p'. */
1.84 brouard 4290: freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);
1.53 brouard 4291:
1.86 ! brouard 4292: if(fileappend(fichtm, optionfilehtm)){
! 4293: fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
! 4294: Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
! 4295: Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
! 4296: imx,agemin,agemax,jmin,jmax,jmean);
! 4297: fclose(fichtm);
! 4298: }
1.60 brouard 4299: pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
4300: oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
4301: newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
4302: savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
4303: oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
1.53 brouard 4304:
4305:
1.59 brouard 4306: /* For Powell, parameters are in a vector p[] starting at p[1]
4307: so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
4308: p=param[1][1]; /* *(*(*(param +1)+1)+0) */
1.53 brouard 4309:
1.86 ! brouard 4310: globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
1.85 brouard 4311: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
4312: printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
4313: for (k=1; k<=npar;k++)
4314: printf(" %d %8.5f",k,p[k]);
4315: printf("\n");
4316: globpr=1; /* to print the contributions */
4317: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
4318: printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
4319: for (k=1; k<=npar;k++)
4320: printf(" %d %8.5f",k,p[k]);
4321: printf("\n");
1.61 brouard 4322: if(mle>=1){ /* Could be 1 or 2 */
1.53 brouard 4323: mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
1.59 brouard 4324: }
1.53 brouard 4325:
1.59 brouard 4326: /*--------- results files --------------*/
4327: fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);
1.53 brouard 4328:
4329:
1.59 brouard 4330: jk=1;
4331: fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
4332: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
4333: fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
4334: for(i=1,jk=1; i <=nlstate; i++){
4335: for(k=1; k <=(nlstate+ndeath); k++){
4336: if (k != i)
4337: {
4338: printf("%d%d ",i,k);
4339: fprintf(ficlog,"%d%d ",i,k);
4340: fprintf(ficres,"%1d%1d ",i,k);
4341: for(j=1; j <=ncovmodel; j++){
4342: printf("%f ",p[jk]);
4343: fprintf(ficlog,"%f ",p[jk]);
4344: fprintf(ficres,"%f ",p[jk]);
4345: jk++;
4346: }
4347: printf("\n");
4348: fprintf(ficlog,"\n");
4349: fprintf(ficres,"\n");
4350: }
4351: }
4352: }
1.84 brouard 4353: if(mle!=0){
1.59 brouard 4354: /* Computing hessian and covariance matrix */
4355: ftolhess=ftol; /* Usually correct */
4356: hesscov(matcov, p, npar, delti, ftolhess, func);
4357: }
4358: fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
4359: printf("# Scales (for hessian or gradient estimation)\n");
4360: fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
4361: for(i=1,jk=1; i <=nlstate; i++){
4362: for(j=1; j <=nlstate+ndeath; j++){
4363: if (j!=i) {
4364: fprintf(ficres,"%1d%1d",i,j);
4365: printf("%1d%1d",i,j);
4366: fprintf(ficlog,"%1d%1d",i,j);
4367: for(k=1; k<=ncovmodel;k++){
4368: printf(" %.5e",delti[jk]);
4369: fprintf(ficlog," %.5e",delti[jk]);
4370: fprintf(ficres," %.5e",delti[jk]);
4371: jk++;
4372: }
4373: printf("\n");
4374: fprintf(ficlog,"\n");
4375: fprintf(ficres,"\n");
4376: }
4377: }
4378: }
1.53 brouard 4379:
1.59 brouard 4380: fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n# ...\n# 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n");
4381: if(mle==1)
4382: printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n# ...\n# 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n");
4383: fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n# ...\n# 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n");
4384: for(i=1,k=1;i<=npar;i++){
4385: /* if (k>nlstate) k=1;
4386: i1=(i-1)/(ncovmodel*nlstate)+1;
4387: fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);
4388: printf("%s%d%d",alph[k],i1,tab[i]);
4389: */
4390: fprintf(ficres,"%3d",i);
4391: if(mle==1)
4392: printf("%3d",i);
4393: fprintf(ficlog,"%3d",i);
4394: for(j=1; j<=i;j++){
4395: fprintf(ficres," %.5e",matcov[i][j]);
4396: if(mle==1)
4397: printf(" %.5e",matcov[i][j]);
4398: fprintf(ficlog," %.5e",matcov[i][j]);
4399: }
4400: fprintf(ficres,"\n");
4401: if(mle==1)
4402: printf("\n");
4403: fprintf(ficlog,"\n");
4404: k++;
4405: }
1.53 brouard 4406:
1.59 brouard 4407: while((c=getc(ficpar))=='#' && c!= EOF){
4408: ungetc(c,ficpar);
4409: fgets(line, MAXLINE, ficpar);
4410: puts(line);
4411: fputs(line,ficparo);
4412: }
4413: ungetc(c,ficpar);
4414:
4415: estepm=0;
4416: fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
4417: if (estepm==0 || estepm < stepm) estepm=stepm;
4418: if (fage <= 2) {
4419: bage = ageminpar;
4420: fage = agemaxpar;
4421: }
1.53 brouard 4422:
1.59 brouard 4423: fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
4424: fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
4425: fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
1.53 brouard 4426:
1.59 brouard 4427: while((c=getc(ficpar))=='#' && c!= EOF){
4428: ungetc(c,ficpar);
4429: fgets(line, MAXLINE, ficpar);
4430: puts(line);
4431: fputs(line,ficparo);
4432: }
4433: ungetc(c,ficpar);
1.53 brouard 4434:
1.59 brouard 4435: fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);
4436: fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
4437: fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
1.69 brouard 4438: printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
4439: fprintf(ficlog,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
1.53 brouard 4440:
1.59 brouard 4441: while((c=getc(ficpar))=='#' && c!= EOF){
4442: ungetc(c,ficpar);
4443: fgets(line, MAXLINE, ficpar);
4444: puts(line);
4445: fputs(line,ficparo);
4446: }
4447: ungetc(c,ficpar);
1.53 brouard 4448:
4449:
1.70 brouard 4450: dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
4451: dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
1.53 brouard 4452:
4453: fscanf(ficpar,"pop_based=%d\n",&popbased);
4454: fprintf(ficparo,"pop_based=%d\n",popbased);
4455: fprintf(ficres,"pop_based=%d\n",popbased);
4456:
4457: while((c=getc(ficpar))=='#' && c!= EOF){
4458: ungetc(c,ficpar);
4459: fgets(line, MAXLINE, ficpar);
4460: puts(line);
4461: fputs(line,ficparo);
4462: }
4463: ungetc(c,ficpar);
4464:
1.69 brouard 4465: fscanf(ficpar,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj);
1.70 brouard 4466: fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
1.71 brouard 4467: printf("prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
4468: fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
4469: fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
1.69 brouard 4470: /* day and month of proj2 are not used but only year anproj2.*/
1.53 brouard 4471:
1.59 brouard 4472: while((c=getc(ficpar))=='#' && c!= EOF){
1.53 brouard 4473: ungetc(c,ficpar);
4474: fgets(line, MAXLINE, ficpar);
4475: puts(line);
4476: fputs(line,ficparo);
4477: }
4478: ungetc(c,ficpar);
4479:
4480: fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);
4481: fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
4482: fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
4483:
1.86 ! brouard 4484: /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);*/
1.84 brouard 4485: /*,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
1.58 lievre 4486:
1.59 brouard 4487: printinggnuplot(fileres, ageminpar,agemaxpar,fage, pathc,p);
1.53 brouard 4488:
1.85 brouard 4489: printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
4490: model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
4491: jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
1.53 brouard 4492:
1.59 brouard 4493: /*------------ free_vector -------------*/
4494: chdir(path);
1.53 brouard 4495:
1.59 brouard 4496: free_ivector(wav,1,imx);
4497: free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
4498: free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
4499: free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
1.85 brouard 4500: free_lvector(num,1,n);
1.59 brouard 4501: free_vector(agedc,1,n);
1.65 lievre 4502: /*free_matrix(covar,0,NCOVMAX,1,n);*/
1.59 brouard 4503: /*free_matrix(covar,1,NCOVMAX,1,n);*/
4504: fclose(ficparo);
4505: fclose(ficres);
1.53 brouard 4506:
4507:
1.54 brouard 4508: /*--------------- Prevalence limit (stable prevalence) --------------*/
1.53 brouard 4509:
4510: strcpy(filerespl,"pl");
4511: strcat(filerespl,fileres);
4512: if((ficrespl=fopen(filerespl,"w"))==NULL) {
1.54 brouard 4513: printf("Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
4514: fprintf(ficlog,"Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
1.53 brouard 4515: }
1.54 brouard 4516: printf("Computing stable prevalence: result on file '%s' \n", filerespl);
4517: fprintf(ficlog,"Computing stable prevalence: result on file '%s' \n", filerespl);
4518: fprintf(ficrespl,"#Stable prevalence \n");
1.53 brouard 4519: fprintf(ficrespl,"#Age ");
4520: for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
4521: fprintf(ficrespl,"\n");
4522:
4523: prlim=matrix(1,nlstate,1,nlstate);
1.59 brouard 4524:
1.53 brouard 4525: agebase=ageminpar;
4526: agelim=agemaxpar;
4527: ftolpl=1.e-10;
4528: i1=cptcoveff;
4529: if (cptcovn < 1){i1=1;}
4530:
1.59 brouard 4531: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
1.53 brouard 4532: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
1.59 brouard 4533: k=k+1;
4534: /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
4535: fprintf(ficrespl,"\n#******");
4536: printf("\n#******");
4537: fprintf(ficlog,"\n#******");
4538: for(j=1;j<=cptcoveff;j++) {
4539: fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4540: printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4541: fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4542: }
4543: fprintf(ficrespl,"******\n");
4544: printf("******\n");
4545: fprintf(ficlog,"******\n");
1.53 brouard 4546:
1.59 brouard 4547: for (age=agebase; age<=agelim; age++){
4548: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
1.69 brouard 4549: fprintf(ficrespl,"%.0f ",age );
4550: for(j=1;j<=cptcoveff;j++)
4551: fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
1.59 brouard 4552: for(i=1; i<=nlstate;i++)
1.53 brouard 4553: fprintf(ficrespl," %.5f", prlim[i][i]);
1.59 brouard 4554: fprintf(ficrespl,"\n");
1.53 brouard 4555: }
4556: }
1.59 brouard 4557: }
1.53 brouard 4558: fclose(ficrespl);
4559:
4560: /*------------- h Pij x at various ages ------------*/
4561:
4562: strcpy(filerespij,"pij"); strcat(filerespij,fileres);
4563: if((ficrespij=fopen(filerespij,"w"))==NULL) {
4564: printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
4565: fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
4566: }
4567: printf("Computing pij: result on file '%s' \n", filerespij);
4568: fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
4569:
4570: stepsize=(int) (stepm+YEARM-1)/YEARM;
4571: /*if (stepm<=24) stepsize=2;*/
4572:
4573: agelim=AGESUP;
4574: hstepm=stepsize*YEARM; /* Every year of age */
4575: hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
4576:
4577: /* hstepm=1; aff par mois*/
4578:
1.70 brouard 4579: fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
1.59 brouard 4580: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
1.53 brouard 4581: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
4582: k=k+1;
1.59 brouard 4583: fprintf(ficrespij,"\n#****** ");
4584: for(j=1;j<=cptcoveff;j++)
4585: fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4586: fprintf(ficrespij,"******\n");
1.53 brouard 4587:
1.59 brouard 4588: for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
4589: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
4590: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
4591:
4592: /* nhstepm=nhstepm*YEARM; aff par mois*/
4593:
4594: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4595: oldm=oldms;savm=savms;
4596: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
1.70 brouard 4597: fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
1.59 brouard 4598: for(i=1; i<=nlstate;i++)
4599: for(j=1; j<=nlstate+ndeath;j++)
4600: fprintf(ficrespij," %1d-%1d",i,j);
4601: fprintf(ficrespij,"\n");
4602: for (h=0; h<=nhstepm; h++){
1.70 brouard 4603: fprintf(ficrespij,"%d %3.f %3.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
1.53 brouard 4604: for(i=1; i<=nlstate;i++)
4605: for(j=1; j<=nlstate+ndeath;j++)
1.59 brouard 4606: fprintf(ficrespij," %.5f", p3mat[i][j][h]);
1.53 brouard 4607: fprintf(ficrespij,"\n");
4608: }
1.59 brouard 4609: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4610: fprintf(ficrespij,"\n");
4611: }
1.53 brouard 4612: }
4613: }
4614:
1.74 brouard 4615: varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax);
1.53 brouard 4616:
4617: fclose(ficrespij);
4618:
1.84 brouard 4619: probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.53 brouard 4620:
4621: /*---------- Forecasting ------------------*/
1.69 brouard 4622: /*if((stepm == 1) && (strcmp(model,".")==0)){*/
4623: if(prevfcast==1){
1.74 brouard 4624: /* if(stepm ==1){*/
1.70 brouard 4625: prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
1.74 brouard 4626: /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
4627: /* } */
4628: /* else{ */
4629: /* erreur=108; */
4630: /* printf("Warning %d!! You can only forecast the prevalences if the optimization\n has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
4631: /* fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
4632: /* } */
1.69 brouard 4633: }
1.53 brouard 4634:
4635:
4636: /*---------- Health expectancies and variances ------------*/
4637:
4638: strcpy(filerest,"t");
4639: strcat(filerest,fileres);
4640: if((ficrest=fopen(filerest,"w"))==NULL) {
4641: printf("Problem with total LE resultfile: %s\n", filerest);goto end;
4642: fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
4643: }
4644: printf("Computing Total LEs with variances: file '%s' \n", filerest);
4645: fprintf(ficlog,"Computing Total LEs with variances: file '%s' \n", filerest);
4646:
4647:
4648: strcpy(filerese,"e");
4649: strcat(filerese,fileres);
4650: if((ficreseij=fopen(filerese,"w"))==NULL) {
4651: printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
4652: fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
4653: }
4654: printf("Computing Health Expectancies: result on file '%s' \n", filerese);
4655: fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
1.68 lievre 4656:
1.53 brouard 4657: strcpy(fileresv,"v");
4658: strcat(fileresv,fileres);
4659: if((ficresvij=fopen(fileresv,"w"))==NULL) {
4660: printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
4661: fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
4662: }
4663: printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
4664: fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
1.58 lievre 4665:
1.74 brouard 4666: /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
1.84 brouard 4667: prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
1.74 brouard 4668: /* printf("ageminpar=%f, agemax=%f, s[lastpass][imx]=%d, agev[lastpass][imx]=%f, nlstate=%d, imx=%d, mint[lastpass][imx]=%f, anint[lastpass][imx]=%f,dateprev1=%f, dateprev2=%f, firstpass=%d, lastpass=%d\n",\
4669: ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
4670: */
1.58 lievre 4671:
1.54 brouard 4672: if (mobilav!=0) {
1.53 brouard 4673: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.54 brouard 4674: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
4675: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
4676: printf(" Error in movingaverage mobilav=%d\n",mobilav);
4677: }
1.53 brouard 4678: }
4679:
1.59 brouard 4680: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
1.53 brouard 4681: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
4682: k=k+1;
4683: fprintf(ficrest,"\n#****** ");
4684: for(j=1;j<=cptcoveff;j++)
4685: fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4686: fprintf(ficrest,"******\n");
4687:
4688: fprintf(ficreseij,"\n#****** ");
4689: for(j=1;j<=cptcoveff;j++)
4690: fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4691: fprintf(ficreseij,"******\n");
4692:
4693: fprintf(ficresvij,"\n#****** ");
4694: for(j=1;j<=cptcoveff;j++)
4695: fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4696: fprintf(ficresvij,"******\n");
4697:
4698: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
4699: oldm=oldms;savm=savms;
4700: evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);
4701:
4702: vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
4703: oldm=oldms;savm=savms;
4704: varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0, mobilav);
4705: if(popbased==1){
4706: varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased,mobilav);
1.59 brouard 4707: }
1.53 brouard 4708:
4709:
4710: fprintf(ficrest,"#Total LEs with variances: e.. (std) ");
4711: for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
4712: fprintf(ficrest,"\n");
4713:
4714: epj=vector(1,nlstate+1);
4715: for(age=bage; age <=fage ;age++){
4716: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
4717: if (popbased==1) {
1.54 brouard 4718: if(mobilav ==0){
1.53 brouard 4719: for(i=1; i<=nlstate;i++)
4720: prlim[i][i]=probs[(int)age][i][k];
1.54 brouard 4721: }else{ /* mobilav */
1.53 brouard 4722: for(i=1; i<=nlstate;i++)
4723: prlim[i][i]=mobaverage[(int)age][i][k];
4724: }
4725: }
4726:
4727: fprintf(ficrest," %4.0f",age);
4728: for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
4729: for(i=1, epj[j]=0.;i <=nlstate;i++) {
4730: epj[j] += prlim[i][i]*eij[i][j][(int)age];
4731: /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
4732: }
4733: epj[nlstate+1] +=epj[j];
4734: }
4735:
4736: for(i=1, vepp=0.;i <=nlstate;i++)
4737: for(j=1;j <=nlstate;j++)
4738: vepp += vareij[i][j][(int)age];
4739: fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
4740: for(j=1;j <=nlstate;j++){
4741: fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
4742: }
4743: fprintf(ficrest,"\n");
4744: }
1.59 brouard 4745: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
4746: free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
4747: free_vector(epj,1,nlstate+1);
1.53 brouard 4748: }
4749: }
1.59 brouard 4750: free_vector(weight,1,n);
4751: free_imatrix(Tvard,1,15,1,2);
4752: free_imatrix(s,1,maxwav+1,1,n);
4753: free_matrix(anint,1,maxwav,1,n);
4754: free_matrix(mint,1,maxwav,1,n);
4755: free_ivector(cod,1,n);
4756: free_ivector(tab,1,NCOVMAX);
1.53 brouard 4757: fclose(ficreseij);
4758: fclose(ficresvij);
4759: fclose(ficrest);
4760: fclose(ficpar);
4761:
1.54 brouard 4762: /*------- Variance of stable prevalence------*/
1.53 brouard 4763:
4764: strcpy(fileresvpl,"vpl");
4765: strcat(fileresvpl,fileres);
4766: if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
1.54 brouard 4767: printf("Problem with variance of stable prevalence resultfile: %s\n", fileresvpl);
1.53 brouard 4768: exit(0);
4769: }
1.54 brouard 4770: printf("Computing Variance-covariance of stable prevalence: file '%s' \n", fileresvpl);
1.53 brouard 4771:
1.59 brouard 4772: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
1.53 brouard 4773: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
4774: k=k+1;
4775: fprintf(ficresvpl,"\n#****** ");
4776: for(j=1;j<=cptcoveff;j++)
4777: fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4778: fprintf(ficresvpl,"******\n");
4779:
4780: varpl=matrix(1,nlstate,(int) bage, (int) fage);
4781: oldm=oldms;savm=savms;
1.59 brouard 4782: varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);
4783: free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
1.53 brouard 4784: }
1.59 brouard 4785: }
1.53 brouard 4786:
4787: fclose(ficresvpl);
4788:
4789: /*---------- End : free ----------------*/
4790: free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
4791: free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
4792: free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
4793: free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
1.65 lievre 4794:
4795: free_matrix(covar,0,NCOVMAX,1,n);
1.53 brouard 4796: free_matrix(matcov,1,npar,1,npar);
1.74 brouard 4797: /*free_vector(delti,1,npar);*/
4798: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
1.53 brouard 4799: free_matrix(agev,1,maxwav,1,imx);
4800: free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
1.54 brouard 4801: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
1.74 brouard 4802: free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
4803:
1.59 brouard 4804: free_ivector(ncodemax,1,8);
4805: free_ivector(Tvar,1,15);
4806: free_ivector(Tprod,1,15);
4807: free_ivector(Tvaraff,1,15);
4808: free_ivector(Tage,1,15);
4809: free_ivector(Tcode,1,100);
1.53 brouard 4810:
1.74 brouard 4811: /* fclose(fichtm);*/
4812: /* fclose(ficgp);*/ /* ALready done */
1.53 brouard 4813:
4814:
4815: if(erreur >0){
4816: printf("End of Imach with error or warning %d\n",erreur);
4817: fprintf(ficlog,"End of Imach with error or warning %d\n",erreur);
4818: }else{
4819: printf("End of Imach\n");
4820: fprintf(ficlog,"End of Imach\n");
4821: }
4822: printf("See log file on %s\n",filelog);
4823: fclose(ficlog);
4824: /* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */
1.85 brouard 4825: (void) gettimeofday(&end_time,&tzp);
4826: tm = *localtime(&end_time.tv_sec);
4827: tmg = *gmtime(&end_time.tv_sec);
4828: strtend=asctime(&tm);
4829: printf("Localtime at start %s and at end=%s",strt, strtend);
4830: fprintf(ficlog,"Localtime at start %s and at end=%s",strt, strtend);
4831: /* printf("Total time used %d Sec\n", asc_time(end_time.tv_sec -start_time.tv_sec);*/
4832:
4833: printf("Total time was %d Sec. %d uSec.\n", end_time.tv_sec -start_time.tv_sec, end_time.tv_usec -start_time.tv_usec);
4834: fprintf(ficlog,"Total time was %d Sec. %d uSec.\n", end_time.tv_sec -start_time.tv_sec, end_time.tv_usec -start_time.tv_usec);
4835: /* printf("Total time was %d uSec.\n", total_usecs);*/
1.86 ! brouard 4836: if(fileappend(fichtm,optionfilehtm)){
! 4837: fprintf(fichtm,"<br>Localtime at start %s and at end=%s<br>",strt, strtend);
! 4838: fclose(fichtm);
! 4839: }
1.53 brouard 4840: /*------ End -----------*/
4841:
1.59 brouard 4842: end:
1.53 brouard 4843: #ifdef windows
4844: /* chdir(pathcd);*/
4845: #endif
4846: /*system("wgnuplot graph.plt");*/
4847: /*system("../gp37mgw/wgnuplot graph.plt");*/
4848: /*system("cd ../gp37mgw");*/
4849: /* system("..\\gp37mgw\\wgnuplot graph.plt");*/
1.59 brouard 4850: strcpy(plotcmd,GNUPLOTPROGRAM);
4851: strcat(plotcmd," ");
4852: strcat(plotcmd,optionfilegnuplot);
1.75 brouard 4853: printf("Starting graphs with: %s",plotcmd);fflush(stdout);
1.59 brouard 4854: system(plotcmd);
1.75 brouard 4855: printf(" Wait...");
1.53 brouard 4856:
1.54 brouard 4857: /*#ifdef windows*/
1.53 brouard 4858: while (z[0] != 'q') {
4859: /* chdir(path); */
4860: printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");
4861: scanf("%s",z);
4862: if (z[0] == 'c') system("./imach");
4863: else if (z[0] == 'e') system(optionfilehtm);
4864: else if (z[0] == 'g') system(plotcmd);
4865: else if (z[0] == 'q') exit(0);
4866: }
1.54 brouard 4867: /*#endif */
1.53 brouard 4868: }
4869:
4870:
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